286 results • Page 1 of 5
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
updated 15 months 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
updated 4.6 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
updated 6.5 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
updated 6 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…
updated 6.3 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 &nbsp;RNAseq of a protein that bind to the 3'UTR of the mRNA. I would like to try to compare the hg…
updated 5.5 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…
updated 5.9 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 &lt;- Rsubread::featureCounts(files=bam,annot.ext=gtf, isGTFAnnotationFile=TRUE,GTF.featureType="exon", GTF.attr…
updated 5.1 years ago • Ge Tan
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…
updated 3.8 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...and featureCounts is running out of memory. Specifically, I'm counting ChIP-Seq reads in bins placed every 50 bp across the entire...is the log output for the crash. Note that "feature…
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)&nbsp;output, so that users don't have to modify the FeatureCounts output to convert into D…
updated 7.4 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 : <…
updated 5.0 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 …
updated 14 months 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 |…
updated 6.4 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
updated 3.2 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…
updated 23 months 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
updated 6 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
updated 8 months ago • margo
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…
updated 2.1 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
updated 8 months ago • Hicham
http://file:///C:/Users/Administrateur/Desktop/featureCounts/counts.txt> &nbsp; I have made the index and did mapping using STAR. Then I used feuture Count to read the count
updated 4.4 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…
updated 3 months ago • rridley3
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: ... &gt; || Load annotation file ~/genomes/mus\_musculus/mm10/annotation/ensembl\_mu ... || &gt;&nbsp;Failed...I would like to use Rsubreads to coutn feature on exon (summarizing at the gene ID level), however featureCounts does not accep…
updated 7.9 years ago • samuel collombet
Hi, &nbsp; 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 (…
updated 4.7 years ago • inah
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 …
updated 6.6 years ago • Jon Manning
Hi all, I use featurecounts first to get the summary of the counts and the annotation, below are the codes: test&lt;-featureCounts(files="test.bam
updated 5.3 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
updated 7.0 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…
updated 2.8 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
updated 5.3 years ago • Ge Tan
Hello,&nbsp; 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…
updated 4.2 years ago • gbreard
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 …
updated 3.9 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...…
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…
updated 3 months ago • dario.beraldi
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 //========================…
updated 12 months 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…
updated 7.2 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,…
Hi, What would be the simple way of telling featureCounts to read a whole folder filled&nbsp;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&nbsp;with BAM files? I am hoping not to have to write a few hundred lines of text in
updated 8.0 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…
updated 4.7 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 &lt;- list.files...pattern="\\.fastq$", full=TRUE) all.bam &lt;- sub("\\.fastq$", ".bam", fastqPath) fc &lt;- featureCounts(all.bam, annot.ext="ThePathofM…
updated 3.8 years ago • Raito92
Hi, I'm using featureCounts to count reads in bam files from RNAseq. Those bam contain the header "@CO This BAM file is processed by rsem-tbam2gam..._____/ \____/|____/|_| \_\______/_/ \_\_____/ v1.6.3 //========================== featureCounts setting ===========================\\ || …
updated 4.0 years ago • leo_CD
div class="preformatted">I am confused by this output from featureCounts(): &gt; dat1 &lt;- featureCounts(fls[1], annot.inbuilt="mm10", useMetaFeatures = TRUE) &gt; head(dat1$annotation) GeneID Chr
updated 9.3 years ago • James W. MacDonald
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&lt;- Rsubread::featureCounts
updated 3.2 years ago • v.shapovalova1
Hi there, I have been using featureCounts for quite some time now and I really like it.&nbsp; However, I have come across a workflow for deconvoluting multimapping...defined in one of the columns ("XF:Z:....")&nbsp; 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…
updated 5.7 years ago • courtney.stairs
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 featureCounts...1.5.1 I am using human samples and the hg19 gtf annotation file. I ran featureCounts after getting unreliable results from htseq-count. My samples are paired, and featureCounts was appealing...after strugglin…
Hi, &nbsp; 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&nbsp; &nbsp; WARNING no features were loaded
updated 6.1 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 …
updated 2.3 years ago • martinag.work
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…
updated 17 months ago • nklier38
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
updated 4.6 years ago • Gary
<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: &gt;…
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 7.2 years ago • Ryan C. Thompson
featureCounts: 0% successfully assigned fragments on PE .BAM files I am facing same problem, performed every suggestion but
updated 8 months ago • KMS
file which i converted to BAM file format. Now i want to count the reads by using Rsubread function featurecounts, This requires gtf annotation file. how can i generate the gtf file for this. Thank you
Hi, I'm using featureCounts (subread v2.0.2) to generate a count matrix for an RNAseq experiment. I have aligned paired-end .sam files sorted...Hi, I'm using featureCounts (subread v2.0.2) to generate a count matrix for an RNAseq experiment. I have aligned paired-end .sam files sorted by read name and have specified the -p flag and the −−countReadPairs parameter (please see code below). Whe…
updated 19 months ago • s.muroy
div class="preformatted">Hi Ryan, Sorry for my late reply. We have added the following options to featureCounts to let users be able to extend reads and also control the overlap length between reads and featureCounts: readExtension5...readExtension3 minReadOverlap The featureCounts help page describes the meaning of these parameters and how to use them. Changes have been committed to bioc.…
updated 8.8 years ago • Wei Shi
Summary** It seems featureCounts under certain circumstances ignores the ```isPairedEnd = TRUE``` argument. **Background** I have been using featureCounts...sam2bed | cut -f 6 | sort | uniq -c 11 - 1272 + ``` So far so good. Now lets try with featureCount from the R package Rsubread **Rsubread::featureCount approach**: ``` library(Rsubread) ### Create regions to…
updated 3.8 years ago • k.vitting.seerup
I'm using the featureCounts function of Rsubread to assign aligned reads to features. Something like ~20% of my reads are unassigned (in...I'm using the featureCounts function of Rsubread to assign aligned reads to features. Something like ~20% of my reads are unassigned (in the
updated 2.7 years ago • am39
I extracted exon information from mm9 and then used it for featureCount. Next I used an in-built mm9 annotation of featureCount and I got less exons annotated somehow. __Extraction...uc007aeu.1 &nbsp; Xkr4</pre> &nbsp; __FeatureCount with the manual exon annotation:__ ​manual=featureCounts(c(bam.CTCF,bam.H3K27ac),annot.ext=exon\_info\_red,isGTFAnnotationFile=FALSE, <p…
updated 7.4 years ago • tonja.r
3 of the SAM files were created from PE data, and 1 SAM file was created from SE data. I want to use featurecounts to create a count matrix, however, should I be using paired end mode or single end mode?&nbsp; Thanks for the help
updated 5.5 years ago • nikelle.petrillo
Hi, &nbsp; I want to obtain read counts at the exon level using featureCounts. I run Rsubread and use these options: annot.ext="/home/inah/RefGTF/GRCh38/annotation/Homo\_sapiens.GRCh38.85.gtf
updated 5.7 years ago • inah
Right now, the result objects from `Rsubread::featureCounts` can easily read into most DE Analysis packages (at least for `DESeq2` and `edgeR`, which should cover most use cases...Right now, the result objects from `Rsubread::featureCounts` can easily read into most DE Analysis packages (at least for `DESeq2` and `edgeR`, which should cover most use cases). However, at this time, it appears to me…
updated 8 months ago • johnmcma
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