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samples into a single BAM, called peaks (Genrich), and counted reads per peak region for each sample (featureCounts). I then ran limma following common guidance (example code below), and the resulting MA plot shows many more significantly

limma edger atac atac-seq

updated 4.2 years ago • pgugger

list=ls()) setwd('H:/qde-2.20191220/DEG/') library("edgeR") Counts data generated by featureCounts program countData <- read.table('qde2_featurecounts',header = TRUE,sep = '\t',row.names = 1) countData <- countData

edgeR no replication glmLRT(fit coef=2)

updated 4.4 years ago • hong1ang

e -B -G ${GTF} -o transcripts.gtf -A gene_abundances.tsv input.rmdup.bam **Deseq2 (using featureCounts counts)** featureCounts -T $threads -p -F GTF -t exon -g gene_id -s 2 -a ${GTF} -o out.featurecount input.rmdup.bam **FPKM values

deseq2 StringTie RNA-seq normalisation

updated 4.4 years ago • JindrichK

with changes in exon usage that I should be able to recapitulate. My strategy was to use featureCounts (Rsubread) in order to get count data for each exon. I generated the flattened gtf using the python script provided...transcripts "ENST00000456328"; exonic_part_number "009" The issue arises when I try to use the featureCount function with these gtfs on their respective datasets. Both data…

dexseq rsubread featureCount software error

updated 4.5 years ago • seung.ho.steven.choi

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 4.5 years ago • v.shapovalova1

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 4.5 years ago • adeler001

I am analyzing an experiment on the mouse olfactory epithelium. We have 3 treatment conditions and 1 control condition. Each condition contains 4 biological replicates. Our 3 treatment conditions each express a different isoform of transgenically up-regulated Adar protein. Adar is hypothesized as a negative regulator of circular RNAs (circRNAs). It's hypothesized mechanism of negative regulation …

deseq2 circRNA rna-editing

updated 4.5 years ago • maxhenryhills

with not problems. Thanks in advance for any help. Best regards, Christian Mertes ``` > featureCounts(file="HG00356.2.M_111215_6.bam", annot.ext=ranges, isLongRead=FALSE) ========== _____ _ _ ____ _____ ______ _____ ===== / ____..._____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 1.34.7 //=======================…

Rsubread counting RNA-seq

updated 4.6 years ago • mertes

I can filter bam file from above command to pass it to feature count. This is what I use right now. featureCounts -p -T 5 -a hg38GENCODE.gtf -o $filename.txt $filename.bam & I am running data in bulk, that requires bwa mem with...above parameters so do not want to use resources for e.g. STAR alignment etc for passing it to featureCount. I am very new to this field, so please d…

bwa mem featureCounts

updated 4.6 years ago • ajajoo

Hello I'm doing an rna seq differential expression analysis using DESeq2 I did the read counting using **FeatureCount** but didn't normalize the read counts after. I just wanted to confirm if I have interpreted the DESeq2 manual statement...I'm doing an rna seq differential expression analysis using DESeq2 I did the read counting using **FeatureCount** but didn't normalize the read counts …

deseq2 rnaseq

updated 4.7 years ago • adeler001

I am using featureCounts for my RNA-seq data to get count matrix. but m facing some problem with my output file. Most of the file is fine...I am using featureCounts for my RNA-seq data to get count matrix. but m facing some problem with my output file. Most of the file is fine but

rna-seq featureCounts SubRead

updated 4.8 years ago • hafiz.talhamalik

Hey, nice package. I have an error using featureCounts with paired end reads: I mapped paired end reads with STAR (trimmed reads with fastp), and wanted to try out Rsubread...counting in R. library(Rsubread) # Define paths to RNA-seq bam file and gtf a <- featureCounts(files = df$RNA[1], annot.ext = gtfAnno, isGTFAnnotationFile = T, isPairedEnd = T, requireBothEndsMap…

Rsubread paired end featureCounts

updated 4.8 years ago • hauken_heyken

I generated a count list using featureCounts of my ATAC-seq data and fed it into R. I got the GC bias and lenght for each peak queried, and made a list for the sequencing

cqn normalization conditionalquantilenormalization atac-seq

updated 4.8 years ago • Eric.Martin

Hello! I can't run featureCounts with gff3 file. Please, help! My **gff3 file** structure is: ``` chr1 . miRNA_primary_transcript 17369 17436 . - . ID=MI0022705...ID=MIMAT0027619;Alias=MIMAT0027619;Name=hsa-miR-6859-3p;Derives_from=MI0022705 ``` **Command line:** ``` ./featureCounts -F -a ./../annotation/hsa_miR.gff3 -o ./../../../projects/vesicles/1_repeat_vesicles/counts_K.txt ./../..…

subread featureCounts gtf/gff/gff3

updated 4.8 years ago • algenubi81

was done by sequencing facility using STAR) and **1) Generated read counts with RSubread featureCounts** ``` counts<-featureCounts(files=c("WGTR_0001_Le_n_WT_OT1DTAM1.merged.sorted.bam", "WGTR_0001_Le_n_WT_OT1DTAM2.merged.sorted.bam

edger

updated 4.9 years ago • melanie.girard

normal）, 2 experimental groups（Esophageal cancer），The result is Figure 1.![Figure 1][1] I use featurecounts to count genes, this is my [counts array][2] [1]: http://chuantu.xyz/t6/702/1558315882x2890202416.png [2]: http://223.94.4.98

deseq2 cancer

updated 5.0 years ago • xuyao15927402897

Setup --- files: /path/to/file/here/file1.bam; /path/to/file/here/file2.bam countData=featureCounts(.....) ------- 1.28.1 --- colnames(countData$counts) [1] file1.bam [2] file2.bam ---- 1.34.0 ---- colnames(countData$counts) [1] X.path.to.file.here.file1.bam

Rsubread featureCounts

updated 5.0 years ago • wunderl

find genes that associate with changes in triglyceride levels (TG) in the liver samples. I used featureCounts to summarize the gene level. ``` > dge <- DGEList(counts=expr) > keep <- filterByExpr(dge) > dge <- dge[keep, , keep.lib.sizes

limma edger

updated 5.0 years ago • anna.cot.anna.cot

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 quantify...prevent the subread printout antisenseQuantUnpaired <- featureCounts( files = bamFiles, annot.ext=antisenseAnnot, isP…

rsubread featureCounts

updated 5.1 years ago • k.vitting.seerup

packages/Rsubread/versions/1.22.2/topics/align I wonder whether the options of the **featureCounts** function could matter too... https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts

align rsubread roche454 rnaseq

updated 5.1 years ago • Raito92

input_format = "FASTQ", output_format="BAM", nthreads=8, output_file = all.BAM) featuresC <- featureCounts(all.BAM, annot.inbuilt="mm10") ``` <pre> //================================= Running ==================================\\ || || || Load annotation file mm10_RefSeq_exon.txt ... …

rsubread featureCounts

updated 5.1 years ago • diego.carvalhoalvarez

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 5.1 years ago • aurel.nagy

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 5.1 years ago • Raito92

res$ensembl, mart = ensembl ) fc$counts are gene IDs and counts from featureCounts function

biomaRt getBM

updated 5.1 years ago • angelica.lindlof

Dear, Currently, I would like to calculate exon counts using package Rsubread 1.32.0, function featurecounts. Inputs: 1. Bam file based on paired end RNA sequencing. 2. Annotation file in GTF format, downloaded from GenCode...Gatk.ApplyBQSR From my point of view, I should be able to run following command: featureCounts( files=inputfile, annot.ext=annotation…

R error software error Rsubread featurecounts

updated 5.1 years ago • edejong

50 human samples. The gencode gtf file was used to map the reads. STAR was used to map and featureCounts was used to generate count data. So, the rownames in my files are ensenbl gene_ids which looks like: `"ENSG00000231251.1

edgeR ENEMBL RefSeq

updated 5.2 years ago • mzillur

Hello, I'm processing RNA-seq data (sampleA, sampleB) with featureCounts, and DE analysis with DESeq2. In the DESeq2 output, there are only baseMean, log2FoldChange... I would like to extract...the expected counts calculated by DESeq2 (already normalized, not the raw read counts from featureCounts). Is there anyone knowing how to extract the expected counts value for each sample? For…

deseq2

updated 5.2 years ago • cwliu2014

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 5.2 years ago • estevemp

Hi , For the following : > fCountsList = featureCounts(props, annot.ext="/patho/to/gtf/GRCh38.gtf", isGTFA nnotationFile=TRUE, nthreads=16, isPairedEnd=TRUE, allowMultiOverlap

normalization

updated 5.2 years ago • memoly101

Hi everybody, I have just started using featuercounts and am new to this. Would you please help me with the folowing: >fls <- dir("/path/to/bam/files/", "bam$") > fls [1] "X_A.bam" > props <- propmapped(files=fls) Error in normalizePath(files, mustWork = T) : path[1]="ENCFF064QSN.bam": No such file or directory I can see that bam files are…

path Rsubread

updated 5.2 years ago • memoly101

Hi all, I am running WGCNA on a set of 129 samples from three timepoints with three diseases and various physiological traits. Unfortunately, due to project logistics, they were not able to be sequenced at the same time, and looking at the module-trait relationship, it looks like there is quite a strong batch effect resulting from various aspects of sequencing. Embarrassing facts: Timepoint…

WGCNA batch effect continuous

updated 5.3 years ago • cats_dogs

Dear List, Our sequencing core recently switched from STAR to Kallisto. The genewise output was given as both TPM values and counts. Gordon Smyth has written that TPMs should not be used as input to EdgeR. In a recent paper (F1000 Research 2016,4:1521) Soneson, Love, and Robinson have presented evidence that the method they call simplesum_avextl for deriving reads-per-gene, from numbers-of-tr…

RNASeq-quantification edgeR TPM

updated 5.3 years ago • raf4

wild type and three knock-out mice. I use STAR 2.5.3a (built-in Partek Flow) for the alignment and featureCounts (Rsubread_1.30.9) for the quantification. The command I run featureCoutns is below. files <- c("Chuong753.bam...Chuong755.bam", "Chuong756.bam", "Chuong757.bam", "Chuong758.bam") rc <- featureCounts(files, annot.ext = "mm10ncbiRefSeqCurated.gtf", …

RNA-Seq featureCounts STAR minMQS mapping quality score

updated 5.3 years ago • Gary

RNAseq analysis. Briefly, I mapped the RNA-seq reads to the reference genome using STAR and I used featureCounts to quantify the reads mapped to the reference genes and found the gene counts. I removed rows that have no counts

deseq2 baseMean differential gene expression rnaseqgene

updated 5.3 years ago • melkile26

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 5.3 years ago • leo_CD

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 5.3 years ago • IRAIA.MAIALEN

so I'm using feature counts from Rsubread and I have the following ERRORs after running: > featureCounts(BAMfiles, annot.ext="//path/to/gff/", isGTFAnnotationFile=TRUE, nthreads=16, isPairedend=TRUE, allowMultiOverlap...multi-overlapping features. Error in file(file, "rt") : cannot open the connection Calls: featureCounts -> read.delim -> read.table …

annotation Rsubread featureCounts

updated 5.3 years ago • memoly101

serif,arial,verdana,trebuchet ms; line-height:1.6">dds <- DESeq(DESeqDataSetFromMatrix(countData=featureCounts[,paste(1:24,"D",sep="")],colData=design,design=~Diagnosis:Age))</span></pre> First comparison is this, and is where I get the

deseq2

updated 5.4 years ago • hmgeiger

vs control). Briefly, I mapped the RNA-seq reads to the reference genome using STAR and I used featureCounts to quantify the reads mapped to the reference genes and found the gene counts. Before I start the deferentially

deseq2 rnaseq differential gene expression featurecounts rnaseqGene

updated 5.4 years ago • melkile26

Hi all,  I have recently posted an Rsubread featurecounts related question, but I have another one, based on a quality control analysis I would like to do:  I am attempting

rsubread alignment align

updated 5.4 years ago • A

Hi all,  I am having a weird issue (weird to me being a new R user) using featurecounts to generate counts for genes but also for individual exons. I have successfully mapped gene counts to their...with total read mapped to genes. The code I am using is as follows: For annotating genes: fc <- featureCounts(bamDir, isGTFAnnotationFile = TRUE, annot.ext = "Mus\_musculus.GRCm38.94…

featurecounts Rsubread ggbio

updated 5.5 years ago • A

cell types. This modification is very broad and not amenable to peak analysis. Therefore I have used featurecounts to count up reads falling in gene-bodies for each gene and sample, and now have a counts matrix of K9me2 enrichment

deseq2 Cut&Run

updated 5.5 years ago • MPerch

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 5.5 years ago • gbreard

Hi, When one have generated counts using FeatureCounts it generates a list of transcripts and note genes. I understand the procotol as "gene"-counts should be used...Hi, When one have generated counts using FeatureCounts it generates a list of transcripts and note genes. I understand the procotol as "gene"-counts should be used - however how is genecounts defined? Can I use the transcript-count…

deseq2

updated 5.6 years ago • SannaG

I'm using featureCounts (from Rsubread R/Bioconductor package) and gencode annotation file to do features sumarization, but the gene

biomart rsubread gencode

updated 5.6 years ago • YinCY

Hi,  I was wondering which counts are appropriate to use for plotting the expression of the differential transcripts? `` plotDEXSeq `` is giving me this error, even when using the pre-constructed matrix of counts from the workflow "__Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification__": plotDEXSeq( dxr2, "ENSG0…

DEXSeq StageR rnaseqDTU

updated 5.6 years ago • rbenel

get a direction about the correct design for my experiment I have counts tables (generated with FeatureCounts) my samples where sorted for 2 markers and I have samples from 2 different tissues (with triplicates). meaning

deseq2 differential gene expression multiple factor design

updated 5.6 years ago • galozs

Dear Team, I want to perform differential expression on counts generated from featureCounts. Each family has different disease. Can we perfrom differential expression across all samples? or since disease

deseq2 multiple factor design

updated 5.6 years ago • vrehaman

nbsp; I have raw counts data from featureCounts. I actually wanted to do survival analysis. For a specific gene I want to classify the samples into Low and High

deseq2 r fpkm() geneexpression

updated 5.6 years ago • Beginner

I want to plot trends between genes across different conditions from my normalized count matrix (featurecount-EdgeR). I was using "csCluster" in cummerbund. Now I switched to this pipeline and I am wondering, if similar pacakage

edger clustering visualization

updated 5.6 years ago • thindmarsmission

I try to analyse RRHP data. I think I have to count my reads for each of my samples. So I used featurecount on my bam files, but I had low coverage... Is anybody have already count reads from DNA seq? Thanks a lot!!! Christelle

RRHP

updated 5.6 years ago • christelle.ledantec

I try to read counts using featurecounts and I have a warning says: could somebody help me to figureout the problem?   Warning: failed to find the gene

featurecounts

updated 5.7 years ago • roghaiyeh.safari

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 5.7 years ago • roghaiyeh.safari

RNA-Seq data for 8 different treatment conditions, with 3 biological replicates for each. I used the featureCounts command on Rsubread and have the raw counts matrix for all 24 samples at the meta-feature(gene) level. I was wondering

differential gene expression biologicalreplicates raw_counts

updated 5.7 years ago • tasnif.rahman

Hi, The options `` read2pos `` and `` readExtension3 `` are usefull for counting fixed fragments (). Recently I considered one condition of counting reads based on their 5' most base, whose position was shifted. For example, the 5' most base is first shifted by a fixed number based on POS and CIGAR fields, then reads are summarized. It is useful if the middle point of fragments are considered in…

featurecounts subread

updated 5.7 years ago • Leon

Hi everyone, I used DESeq2 for DE analysis of featureCounts data from RNAseq of 2 treatments (A & B) with 2 replicates each. I have the same error as in this thread: https...Hi everyone, I used DESeq2 for DE analysis of featureCounts data from RNAseq of 2 treatments (A & B) with 2 replicates each. I have the same error as in this thread: https://support.bioconductor.org...vari…

deseq2 featurecounts error message

updated 5.7 years ago • Yuqia

More perplexingly, they have 100% sequence identity with a single gene. My question, then, is why featureCounts is failing to map these sequences? I've thought to change the stringency settings, but I doubt that will make

featurecounts rnaseq subread

updated 5.7 years ago • rogangrant

No such file or directory</pre> But Rsubread is installed: <pre> library(Rsubread) featureCounts() NCBI RefSeq annotation for mm10 (build 38.1) is used. Error in paste(files, collapse = ";") : argument "files" is missing

dupradar rsubread

updated 5.8 years ago • b.nota

Hello,  I am working on quantifying RNASeq data at the exon level, which is intended for use in the DEXSeq package. I followed the documentation provided in the DEXSeq tutorial (http://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.pdf, page 23), as well as the commands on Subread to DEXSeq helper code (https://github.com/vivekbhr/Subread\_to\_DEXSeq). …

subread featurecounts dexseq rnaseq

updated 5.8 years ago • jennyl.smith12

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 5.9 years ago • hwu12