Data Input for IsoformSwitchAnalyzeR

[jchelbling]

Hi Kristoffer,
My question to you or the community is about data input for IsoformSwitchAnalyzeR.
I am not an Bio-informatic expert because I m more biologist than IT but I m using DEXseq for my own project to characterize exon usage and I think it is a super opportunity to follow my investigation with ISAR to investigate enrichment of my transcript (isoform) of interest (if I understood well).

So,
I got a file called DEXSeq_counts.out which I used for my DEXseq DEU analysis from this sbatch:

#!/bin/bash
module load bioinfo/Subread/2.0.4
featureCounts -f -O -s 2 -p -T 4 -F GTF -t exon -a /home/jhelbling/work/2022-114_GRCm39.109/Results.GRCm39.109_2022.114_All_Trimming_DNAgRMVconta_All/hisat2/Mus_musculus.GRCm39.109_ForFeatureCounts.gtf \
-o DEXSeq_counts.out \
Ip-RNA-1.markdup.sorted.bam \
Ip-RNA-2.markdup.sorted.bam

Does it possible to use output from featurCounts for IsoformSwitchAnalyzeR?
I did not see any possibility in your manual and I m not sure to do it with my output because when I explored my DEXSeq_counts.out file I did not see any transcript_id whithin:

> head DEXSeq_counts.out
# Program:featureCounts v2.0.4; Command:"featureCounts" "-f" "-O" "-s" "2" "-p" "-T" "4" "-F" "GTF" "-t" "exon" "-a" "/home/jhelbling/work/2022-114_GRCm39.109/Results.GRCm39.109_2022.114_All_Trimming_DNAgRMVconta_All/hisat2/Mus_musculus.GRCm39.109_ForFeatureCounts.gtf" "-o" "DEXSeq_counts.out" "Ip-RNA-1.markdup.sorted.bam" "Ip-RNA-2.markdup.sorted.bam"
Geneid  Chr     Start   End     Strand  Length  Ip-RNA-1.markdup.sorted.bam     Ip-RNA-2.markdup.sorted.bam
ENSMUSG00000102693      1       3143476 3144545 +       1070    0       0
ENSMUSG00000064842      1       3172239 3172348 +       110     0       0
ENSMUSG00000051951      1       3276124 3276745 -       622     81      90
ENSMUSG00000051951      1       3276746 3277540 -       795     44      79
ENSMUSG00000051951      1       3283662 3283831 -       170     35      28
ENSMUSG00000051951      1       3283832 3284704 -       873     107     112
ENSMUSG00000051951      1       3284705 3285855 -       1151    124     96
ENSMUSG00000051951      1       3285856 3286567 -       712     77      114

I did not see any transcript_id (might be the issue)

Do you have any suggestion to use featurecounts output for ISAR or any sugestion to get transcript_id from featurecount mapping?

Thanks for your comments reply in advance and apologize for my computation ignorance ;-)

-Jc