Featurecounts exon output

[R adele]

Hello I have the read count per exon, generated by featurecounts. However I’m having trouble interpreting the output file. It list the exon read count for all the transcripts of each gene but it doesn’t indicate which transcript it is , how can I tell which transcript I’m looking at. It also doesn’t label which exon I’m looking at, how can I tell this ?

[Yang LIAO]

When you run featureCounts on the exon mode (with "-f"), you will have the coordinates of exons corresponding to the read counts, hence you can tell which count is for which exon.

If you want to know the transcript identities of the exons, you can specify "--extraAttributes transcript_id" to ask featureCounts reporting the transcript id associated with the exon. However, you must deal with the same or overlapping exons in different transcripts. By default, featureCounts assigns a read to no exons if the read overlaps with multiple exons, but this behaviour can be less favourable to your analysis. You may specify the "-O" option asking featureCounts to assign those reads to all their overlapping exons, or "-O --fraction" to assign only a fractional count. The "--largestOverlap" option may be also useful but it is all dependent on the analysis you want to do. It is highly suggested to read the manual for choosing the best combination of options: 

https://bioconductor.org/packages/release/bioc/vignettes/Rsubread/inst/doc/SubreadUsersGuide.pdf

[R adele]

Hello Yang I  applied the  "--extraAttributes transcript_id" command your suggested . but when I ran the script , it said the command was not recognized please see my script below:

#!/bin/bash

#PBS -N family_13_01_featureCount

#PBS -l nodes=2:ppn=8

#PBS -l vmem=32g

#PBS -l walltime=48:00:00 

#PBS -joe /hpf/projects/eheon/sequencing_repository/raw_fastq/RNA_rabiat/bam

#PBS -l mem=32g

set -euxo pipefail

cd /hpf/projects/eheon/sequencing_repository/raw_fastq/RNA_rabiat/bam

/hpf/tools/centos6/subread/1.5.3/bin/featureCounts -a /hpf/projects/eDeon/sequencing_repository/raw_fastq/RNA_tabiat/bam/gencode.v19.annotation.gtf -o family_13_01_exons_RNA-seq_sorted.counts -p -t exon -s 2 -T 12 -f -O -M --extraAttributes transcript_id D4775_R312_BAligned.sortedByCoord.out.bam D4754_R311_BAligned.sortedByCoord.out.bam D4776_R310Aligned.sortedByCoord.out.bam D4777_R307Aligned.sortedByCoord.out.bam D4778_R308BAligned.sortedByCoord.out.bam D4828_R309_BAligned.sortedByCoord.out.bam 

[Yang LIAO]

It appears that you're using Subread-1.5.3, which is a little out-of-date and doesn't have this option.

It is suggested to use the latest version of the Subread package for analysis.

[R adele]

which subread version would you recommend?

[Yang LIAO]

You can use our latest version:  https://sourceforge.net/projects/subread/files/subread-2.0.0/

[R adele]

ok thanks