Bioconductor Forum

Hello, Does anyone know if theres a way for featureCounts to analyse bam files in parallel? I have been running featureCounts for my bam files and its taking so long ( currently

counts subread RNASeq featurecounts

updated 2.4 years ago • Beth_b

Hi, I am using the linux version of featureCounts, and I would like to count the number of reads in CDS, 5'UTR and 3'UTR. I was wondering if I should just count three...times like: `` featureCounts -t CDS -g gene_id -a $GTF -o counts.txt $BAM `` `` featureCounts -t five_prime_UTR -g gene_id -a $GTF -o counts.txt $BAM `` `` featureCounts

featurecounts

updated 5.8 years ago • hwu12

for this software! Is there any thought of introducing the windowed mode into the subread software featureCounts. Perhaps this is the wrong forum to ask :) Of course defining the windows isn't too problematic. Anyhow, what I really...would appreciate would be a constructor parsing an featureCounts file and returning a RangedSummarizedExperiment object that could be used with csaw. Best, Karl

windowcounts featurecounts

updated 7.7 years ago • karl.nordstrom

Hello! I am trying to run featureCounts v1.6.2 to use for DESeq2. I am running the following command: ./featureCounts -T 8 -s 2 -t gene -o /bighome/lastarr/Practice_DA_RNAseq...featureCounts/input.counts.txt -a /bighome/lastarr/c_elegans.PRJNA13758.WS285.canonical_geneset.gtf /bighome/lastarr

DESeq2

updated 21 months ago • lastarr

Hi, I'm using featureCounts from the Rsubread package. But I have a question about the gene length returned by featrureCounts. I've read...target="_blank">http://bioinf.wehi.edu.au/RNAseqCaseStudy/</a>, and the combination of featureCounts and edgeR is wonderful. We often need to get the R/FPKM values from a RNAseq experiment, and I just used the rpkm...function in edgeR. This func…

featurecounts rnaseq rsubread

updated 7.5 years ago • niuyw

Hi! I'm new in the bioinformatic world so, maybe, this is commonly known in the comunity but I couldn't find anything in the RSubread package instructions... I know that featureCounts have an in-built hg38 genome. For most of my purposes it works great but I have some Immunoprecipitation and  RNAseq of a protein that bind to the 3'UTR of the mRNA. I would like to try to compare the hg…

featurecounts R

updated 6.7 years ago • joangibert14

Dear devs, I am working with the latest version of featureCounts program (1.5.2), and especially on RIBO-seq data. I do need to reduce reads to one position. To do so, I use the very...the position to the P-site of the ribosome (+12 from the 5' end), and I was wondering me that, does featureCounts has a solution to use __--read2pos INT__? In my case, INT = 12, and all reads will be reduced to on…

featurecounts

updated 7.1 years ago • Glihm

Hi, I encountered segfault when calling featurecounts with Ensembl GRCh37 gtf file. In my dataset, only one bam file has the segfault, not the others. And if I use featurecounts...1 mh=TRUE dup=FALSE paired=FALSE threads=8 foo1 <- Rsubread::featureCounts(files=bam,annot.ext=gtf, isGTFAnnotationFile=TRUE,GTF.featureType="exon", GTF.attr…

rsubread featurecounts

updated 6.3 years ago • Ge Tan

analysis; I got the mouse GTF file from NCBI). I have attached screenshots of the summary of the featureCounts process as well as the .txt file I received as an output. Most of the columns of the .txt file look normal but there...txt to .xlsx in R. Am I missing something in this conversion or is there something wrong with my featureCounts output file? As you can see from the attachment, it did no…

GenomeWideAssociation countsimQC RNASeq

updated 7 weeks ago • ryann

I'm trying to count paired end ATAC-seq alignments that fall within peaks specified by a BED file for differential accessibility analyses across two conditions. Peaks were called using `MACS2` with `--shift -75 --extsize 150 --nomodel --keep-dup all --SPMR`, to center reads around sites of transposase insertion. My question is about applying `featureCounts` to identify the number of transposition…

subread featurecounts atac

updated 5.0 years ago • aurel.nagy

div class="preformatted">Hi Wei, I've been testing out the new arguments for featureCounts on my use case, and I'm getting a segfault when I try to run it. I suspect that I may be using a too large annotation...is the log output for the crash. Note that "featureCounts.fragments is my function that simply calls featureCounts with the appropriate arguments. In any case, the crash seems to happe…

Annotation BSgenome BSgenome Rsubread Annotation BSgenome BSgenome Rsubread

updated 9.9 years ago • Ryan C. Thompson

Dear DEXSeq and FeatureCounts team I was wondering if it is possible to better integrate DEXSeq with featureCounts (either the RSubread...Dear DEXSeq and FeatureCounts team I was wondering if it is possible to better integrate DEXSeq with featureCounts (either the RSubread or the command line version) output, so that users don't have to modify the FeatureCounts output to convert into D…

dexseq featurecounts

updated 8.6 years ago • Vivek.b

Hello everybody (maybe it's not the good place for this question), I'm running featureCounts (version 1.6.0, __C code__) with an annotation in SAF format, this way : <pre> /home/marc/Downloads/subread-1.6.0...Hello everybody (maybe it's not the good place for this question), I'm running featureCounts (version 1.6.0, __C code__) with an annotation in SAF format, this way : <…

featurecounts read counting

updated 6.2 years ago • marc.gabriel.01

anyone know where to download the human Annotating Genomes with GFF3 or GTF files or the function featureCount download it automatically in the command line. I did the unpaired end alignment using hg38 reference genome...My objective is to quantify read counts in the bam file using featureCounts. featureCounts -t exon -g gene_id -a annotation.gtf -o counts.txt mapping_results_SE.bam …

ExomeSeq featureCount

updated 2.4 years ago • Do it!

Hi I have been trying to run featureCounts on my mapped bam extension files with the command: featureCounts -s 2 -t exon -g gene\_id -a /oasis/.../genes\_l2.gtf -o...__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.5.1 //========================== featureCounts setting ===========================\\ || || || Input files : 1 BAM file || || P FF1\_1\_R.bam |…

featurecounts rnaseq

updated 7.6 years ago • shg018

Hello I used FeatureCounts to do the read counts for my RNAseq data . Do the read counts FeatureCounts provide an average or absolute total

featurecounts RNAseq

updated 4.4 years ago • adeler001

The size of the bam files, generated by STAR , ranges from 1G to 27GB. Now I am using featureCounts to count reads to genes. I run featurecounts in shell command line with 24 thread machine. This is code that I...used sinteractive --cpus-per-task=24 --mem=120g module load subread featureCounts -p -T 24 -t exon -g gene_id -a genes.gtf -o P11_AM_Left_BAL_6h.txt P11_AM_Left_BAL_6h.Aligned…

RNAseq123

updated 3.1 years ago • demirkalecy

Hi, I read in this site that gff3 format is also acceptable for featureCounts and I don't have gtf but only gff3 file, but it doesn't work. ``` featureCounts -T 6 -t exon -g gene_id -Q 30 -F GTF -a medtr.R108_HM340.gnm1.ann1.85YW.gcv_genes.gff3

gtf/gff3 subread featureCounts

updated 21 months ago • selmanurkeskin

I am trying to perform a count per gene analysis using featureCounts in R. I have downloaded the gtf file and edited it within R to only contain the gene ID, chr, start, end, and strand...within a data frame (df2). I am trying to run featureCounts on df2 with my 6 bam files, however, I am unable to download the package Rsubread. ``` library("Rsubread") Error in library

featureCounts RNASeq Rsubread R

updated 23 months ago • margo

Hello, I have a rather simple question: featureCounts has a long-read mode ("isLongRead" parameter). How does this parameter affect the counting behavior of featureCounts

Rsubread LongRead

updated 6 months ago • mmisak

we have any contamination by ribosomal or other repetitive sequences in our RNA-seq data. However, featureCounts is running extremely slowly on this dataset. Specifically, with only two normal-sized RNA-seq samples, featureCounts...was still running after 16 hours, at which point I aborted it. In contrast, when I run featureCounts on the set of all human exons grouped by gene (a similar-sized ann…

rsubread featurecounts

updated 3.4 years ago • Ryan C. Thompson

As I know, to use DESeq2 you need raw counts. but in my case I have featureCounts. is the raw counts like feature ones ? if not is there a way to convert featureCounts to raw counts in R

deseq featurecounts counts DESeq2

updated 23 months ago • Hicham

http://file:///C:/Users/Administrateur/Desktop/featureCounts/counts.txt>   I have made the index and did mapping using STAR. Then I used feuture Count to read the count

featurecounts star

updated 5.6 years ago • roghaiyeh.safari

Hi, I am currently running FeatureCounts following mapping meta-transcriptomic data back to various reference genomes. I have predicted genes using...CDS 47 1186 127.9 - 0 ID=1_1;partial=00;[…] I looked to run featurecounts using parameters -t CDS, -p, and -g ID for this file, and it did not map any reads. However, when I use the NCBI downloaded...and this file maps 52% of th…

RNASeq FeatureCounts Rna

updated 18 months ago • rridley3

I am using v2.0.6 of `featureCounts` on a Linux machine. I am running the following command: ``` $ subread-2.0.6-Linux-x86_64/bin/featureCounts -a fc_test.saf...NC_086317 ``` And run the following command: ``` $ subread-2.0.6-Linux-x86_64/bin/featureCounts -a fc_test.saf -F SAF -o fc_test.counts.out -T 2 -p -A aliases.txt fc_test.bam ``` Still, I see that none of the alignments...from th…

featureCounts subread Rsubread

updated 28 days ago • vkkodali

Hi, I would like to use Rsubreads to coutn feature on exon (summarizing at the gene ID level), however featureCounts does not accept my gtf: ... > || Load annotation file ~/genomes/mus\_musculus/mm10/annotation/ensembl\_mu ... || > Failed...I would like to use Rsubreads to coutn feature on exon (summarizing at the gene ID level), however featureCounts does not accep…

rsubread featurecounts

updated 9.1 years ago • samuel collombet

Hi all, I'm counting reads to features, using featureCounts() via Rsubread, which is very nice, and fast- thank you. For a particular application I need my variable-length...Hi all, I'm counting reads to features, using featureCounts() via Rsubread, which is very nice, and fast- thank you. For a particular application I need my variable-length, single...features, as in the IntersectionStrict …

rsubread featurecounts summarizeoverlaps

updated 7.8 years ago • Jon Manning

Hi,   I have human total RNA-seq data (PE, Next-Seq) from a pilot study with two samples and am getting results from featureCounts that do not make any sense to me. I process the data as follows: (1) I perform adapter trimming using ea-utils mcf and mild quality trimming using btrim. I use STAR for alignment to the genome. STAR tells me that the first sample has 99,018,190 input reads (…

RNA-seq featureCounts total RNA

updated 5.9 years ago • inah

Hi all, I use featurecounts first to get the summary of the counts and the annotation, below are the codes: test<-featureCounts(files="test.bam

rnaseq annotation featurecounts

updated 6.5 years ago • Jack

Hi, I have used featurecounts to get read counts on my RNAseq libraries. How can I compile results from different libraries for edgeR input

featurecounts edger

updated 8.2 years ago • myprogramming2016

Using the `chrAliases` flag in Rsubread featureCounts is not working as expected. Single-end reads mapped to genome file ftp://ftp.ncbi.nlm.nih.gov/genomes/all...Using the `chrAliases` flag in Rsubread featureCounts is not working as expected. Single-end reads mapped to genome file ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA...GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.gtf.g…

Rsubread

updated 4.0 years ago • kathleen.e.grogan

I have Rsubread 1.26.1 installed in order to do featureCounts with `` byReadGroup=TRUE ``. But featureCounts complains with "No read groups are found; no output is generated". || Process

rsubread featurecounts

updated 6.5 years ago • Ge Tan

Hello,  I am running STAR analysis of RNAseq samples on a Mac Terminal and I can go through the mapping and .bam file generation but when I launch my command featureCounts, I get in jam with a message "GZIP ERROR:-2" scrolling down and I can't stop the process with usual "Ctrl + C" . It seems to...Mac Terminal and I can go through the mapping and .bam file generation but when I launch m…

software error rnaseq

updated 5.4 years ago • gbreard

the 4 count files but omit any row that do not appear in all 4 files. Any help would be appreciated. ``` featureCounts -T 5 -p -t exon -g gene_id -a panTro6.ncbiRefSeq.gtf -o panTro6_counts.txt bam1 bam2 bam3 bam4 bam5 bam6 bam7 featureCounts...t exon -g gene_id -a panPan3.ncbiRefSeq.gtf -o panPan3_counts.txt bam1 bam2 bam3 bam4 bam5 bam6 bam7 featureCounts -T 5 -p -t exon -g gene_id -a ponAbe3.…

rnaseqGene

updated 22 days ago • Christian

Hello dear Bioconductor support group, I am having problems with importing this data results from featureCounts, which output has this format: Program:featureCounts v1.6.2; Command: ``` featureCounts -L file.sam -g Parent -a file_exon.gff...after more than 1000 lines I have the counts and the rest of the information; and I thought the featureCounts format would gave me each result in the …

Rsubread featureCounts

updated 5.1 years ago • estevemp

Hello, I am having trouble getting an output file in Rsubreads using featureCounts. I want to set up my data to run analysis of differential expresssion in EdgeR. I'm running about 40 .bam files...Hello, I am having trouble getting an output file in Rsubreads using featureCounts. I want to set up my data to run analysis of differential expresssion in EdgeR. I'm running about 40 .bam files in...…

RNAseq R Rsubread featurecounts RNASeq

updated 17 months ago • Jon

Using featureCounts v2.0.1, I don't see any effect in changing `-d` and `-D` options (minimum and maximum fragment/template length, respectively...Here's example output using silly values of `-d 10 -D 10000` and `-d 10000 -D 10`. No difference: ``` featureCounts -d 10 -D 10000 -a genrich/ATACseq/single/atac_merge.gff -o tmp.tsv -t peak -g locus_id -p bwa/Ap2oGFP1o.pb.bam cat...0 Unassigne…

subread featureCounts

updated 18 months ago • dario.beraldi

When featureCounts is used to count miRNAs present in genome aligned bam files, it gives miRNA size outputs, as well as long fragments...ie 8kb). I think this is happening because overlapping miRNAs exist, and thus featureCounts cannot distinguish where an individual miRNAs starts and ends in this situation (when there is an overlap...some genomes there are 0 known miRNAs). Thus I have the follo…

featureCounts Rsubread

updated 11 weeks ago • tjgray4

there, Excellent package! I am using it to do RNA-seq. But I encountered a small problem when using featureCounts(). The code is as follows: ```r featureCounts( "A1.raw_1.fastq.gz.subjunc.BAM", annot.inbuilt = NULL, annot.ext = "GCF_015227675.2_mRatBN7.2_genomic.gtf...__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.8.0 //========================…

Rsubread

updated 2.2 years ago • Zhaoxu

I was using featureCounts function from the R package ("Rsubread"). I need to count reads which are mapped to multiple regions but want to...n= number of alignments). However I am unable to find the argument 'fraction' in the R function featureCounts. DEseq2 doesn't take fraction values, do you suggest to round up those values? if yes then can we implement that...in featureCounts. Thank you for…

rsubread

updated 8.4 years ago • tg369

like to know if there is a way to change stringtie "gene_id" with "ref_gene_id" when performing featureCount to construct the count table for edgeR. The thing is that I have use stringtie to create a merged gtf file, using...all the files I want to compare in the DEG analysis. After that I have use featureCount to create the count matrix, and as featureCount uses gtf file "gene_id" by default,…

featureCount rna-seq gene_id re_gene_id stringtie

updated 5.2 years ago • IRAIA.MAIALEN

Since I had forgotten to output the BAM file, I mapped again using only STAR. However when I run featureCounts, for the same sample: ``` featureCounts(files = BAM1, isPairedEnd = TRUE, allowMultiOverlap = TRUE, countMultiMappingReads...and the log looks the same as mentioned above. This time I outputted the .genome.bam file, and for featureCounts: ``` feat…

RNASeqData Rsubread mapping featurecounts

updated 8 months ago • vitoriastavis

Hi, What would be the simple way of telling featureCounts to read a whole folder filled with BAM files? I am hoping not to have to write a few hundred lines of text...Hi, What would be the simple way of telling featureCounts to read a whole folder filled with BAM files? I am hoping not to have to write a few hundred lines of text in

featurecounts

updated 9.2 years ago • Sylvain Foisy

Hello, I have been working my way through learning Rsubread, and I am stuck on the featureCounts() command. The data maps to the reference genome above 90% for these 5 test samples: <pre> NumMapped PropMapped...Hello, I have been working my way through learning Rsubread, and I am stuck on the featureCounts() command. The data maps to the reference genome above 90% for these 5 test samp…

rsubread featurecounts

updated 5.9 years ago • connor.geraghty

workflow to process some RNASeq data. I've tried to create the required matrix of counts through the featureCounts function from Rsubread, by using an external reference genome. That's the code I used. fastqPath <- list.files...pattern="\\.fastq$", full=TRUE) all.bam <- sub("\\.fastq$", ".bam", fastqPath) fc <- featureCounts(all.bam, annot.ext="ThePathofM…

featureCounts rnaseq Rsubread

updated 5.0 years ago • Raito92

Hi, I'm using featureCounts to count reads in bam files from RNAseq. Those bam contain the header "@CO This BAM file is processed by rsem-tbam2gam..._____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //========================== featureCounts setting ===========================\\ || …

subread featureCounts

updated 5.2 years ago • leo_CD

reads from Nanopore(kit RNA002, U-based fastq), I aligned them with minimap2 and tried to count with featureCounts. The reference was transcriptome from https://www.gencodegenes.org/human/. my command was fc<- Rsubread::featureCounts

software error annotation

updated 4.4 years ago • v.shapovalova1

div class="preformatted">I am confused by this output from featureCounts(): > dat1 <- featureCounts(fls[1], annot.inbuilt="mm10", useMetaFeatures = TRUE) > head(dat1$annotation) GeneID Chr

GO GO

updated 10.5 years ago • James W. MacDonald

Hi there, I have been using featureCounts for quite some time now and I really like it.  However, I have come across a workflow for deconvoluting multimapping...defined in one of the columns ("XF:Z:....")  Is it possible to have the read information from featurecounts output to a SAM file? Thanks a lot! Courtney example of htseq-counts SAM file output where GENE\_id will be…

featurecounts SAM htseqcounts

updated 6.9 years ago • courtney.stairs

Hello, I'm trying to use featureCounts to annotate a long read dataset obtained from nanopore sequencing. I noticed from the results reads that...Hello, I'm trying to use featureCounts to annotate a long read dataset obtained from nanopore sequencing. I noticed from the results reads that are...reads were assigned to all 3 ACTG1 isoforms. ![enter image description here][1] I was runni…

featureCounts Rsubread

updated 10 weeks ago • Alex

I apologize in advance for my ignorance--this is my first time using both STAR and featureCounts. my STAR command is STAR --runThreadN 4 --genomeDir $REF --readFilesIn ${FILE1} ${FILE2} --sjdbGTFfile $GTF --outSAMtype...Unsorted --outFileNamePrefix ${OUT\_STAR} my featureCounts command is featureCounts -T 2 -p -t exon -g gene\_id -a ${GTF} -o counts.txt ${FILE1} I am using STAR 2.5.2b and feat…

featurecounts bioconductor differential gene expression star

updated 7.2 years ago • gregory.l.stone

Hi,   I am trying to count the number of genes with featureCounts (subread1.5.1-source). I use -a my annotation.gff but it gives me error    WARNING no features were loaded

differential gene expression

updated 7.3 years ago • esu2001

HI, I'm using featureCounts (a sw provided by the Subread package) to count reads taken from a BAM file without the SEQ - QVAL fields. The read...summation routine gives the expected results with the following parameters: featureCounts -M -a data/basicAnnotation.gtf -o result/basic_M.FC data/basic.bam. I’m wondering if the absence of the SEQ/QVAL...be an issue when using any of the other …

Rsubread featureCounts

updated 3.5 years ago • martinag.work

Hi, I used STAR, featureCounts, and edgeR for RNA-Seq alignment, quantification, and differentially expressed analysis. Could you teach...Hi, I used STAR, featureCounts, and edgeR for RNA-Seq alignment, quantification, and differentially expressed analysis. Could you teach me

featurecounts edgeR

updated 5.8 years ago • Gary

I am using featureCounts to try and create a count table for some RNA-Seq data I collected using an Oxford Nanopore platform. I have .sam...files aligned with minimap2, and am running the following command to try to get a count table: ``` featureCounts -a knownGene_v36.gtf -o countFile *.sam -L ``` Both the GTF file I am using, and the reference genome that the alignments...problem with t…

RNASeq featureCounts

updated 2.6 years ago • nklier38

Ensembl/Gencode GRCh38 for mapping total RNA-Seq projects with STAR, and then counted reads with the featureCounts command from Subread or Rsubread. We are attempting to set up new pipelines with the latest release 43 (GRCh38.p13...differ (NC_060930.1). What (if any) modifications can be made to run Subread or RSubread featureCounts on the new NCBI release and obtain counts data for all ~57 th…

CHM13v2.0 featureCounts T2T Rsubread

updated 13 months ago • Hilary

div class="preformatted">Hello, I would like to request a simple feature for Rsubread's featureCounts function that would make it more useful for ChIP-Seq applications. I want to use featureCounts to count the...sequenced is not representative of the fragment length. Would it be possible to add a parameter to featureCounts to allow this adjustment? Also, an additional feature that would be ni…

updated 8.4 years ago • Ryan C. Thompson

Hello all, From my understanding of the featureCounts manual it should, by default, count reads that align to the features (exons) of a meta-feature (gene). However my...Hello all, From my understanding of the featureCounts manual it should, by default, count reads that align to the features (exons) of a meta-feature (gene). However my output...file is at the exon level (sorry for the…

GeneExpression

updated 12 months ago • CDSPARKS

<div class="preformatted">Hi Sheng, Please keep your post on the list. This is a rather arbitrary choice. You may play with different cutoffs to see what the difference it makes for your data, but a cutoff of 5 or less seems to be quite low to me. I dont really think genes with only 5 reads or less are of interest. Best wishes, Wei On Jul 6, 2013, at 7:38 AM, Sheng Zhao wrote: >…

Sequencing Annotation Rsubread Sequencing Annotation Rsubread

updated 10.8 years ago • Wei Shi

requested in a [previous post](https://support.bioconductor.org/p/83968/)). From reading the featureCounts documentation, I suspected that this would be accomplished by setting the `nonOverlap` parameter, described...to 0. For the rest of the post, I will be discussing the results when using the following call to featureCounts (where the goal was to assign reads to a gene with which it completely…

featureCounts Rsubread

updated 18 days ago • isaac.vock