I am writing that post after several days of researches.
My aim seemed simple because It’s sounds to me like a habits for probably a large number of you. Here is my problem:
During our transcriptomic lessons, we aligned and mapped Arabidopsis’ rna-seq reads into a transcriptome (Bowtie + Tophat). Because I decided to learn and discover the exon-based alternative splicing EdgeR tool, I tried to generate the exon-based matrix count for my .bam files.
From there, I’m paralyzed. I just got 0 count whatever I do, and I can’t find explicit documentation to learn my mistake.
I drop you my code below:
My Arabidopsis.gff3 few lines
|1||araport11||gene||3631||5899||.||+||.||ID=gene:AT1G01010;Name=NAC001;biotype=protein_coding;description=NAC domain-containing protein 1 [Source:UniProtKB/Swiss-Prot%3BAcc:Q0WV96];gene_id=AT1G01010;logic_name=araport11|
My featureCounts code
featureCounts -p -s 2 -T 5 -f -t exon -g exon_id -a Arabidopsis.gff3 -o counts_output.txt output_[% basename %]/accepted_hits.bam
Finally, my output after 0.14 min running
I would be so cheerfull If some can help me to solve that problem, parlty because I really put myself in this and, at this time, I have no more idea to achieve my aim
Thanks for your time!