I am working on stickleback RNAseq data. I want to count reads for each gene. But i am not getting Successfully assigned reads in featurecount. The .gtf file i am using from
Can anyone let me know if the .gtf file is workable?
Please add code and summary statistics, anecdotal descriptions are hard to debug.
I have used this code
featureCounts -T 5 -t exon -g gene_id -O -a reference_trans/corrected.gtf -b -o Counts_SRR1390636.txt SRR1390636_sorted.bam
Output description link below
enter link description here
Ok, did you check if the chromosome names are the same between your BAM and your GTF?
Chromosomes name of these two files are different.
There is your reason why nothing can be mapped.
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