Gtf/gff file in featurecounts

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4.6 years ago

baurumon ▴ 30

Hello, 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

ftp://ftp.ensembl.org/pub/release-100/gtf/gasterosteus_aculeatus/

Can anyone let me know if the .gtf file is workable?

rna-seq • 3.2k views

ADD COMMENT • link 4.6 years ago by baurumon ▴ 30

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Please add code and summary statistics, anecdotal descriptions are hard to debug.

ADD REPLY • link 4.6 years ago by ATpoint 85k

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Hi 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

enter image description here

Thanks

ADD REPLY • link 4.6 years ago by baurumon ▴ 30

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Ok, did you check if the chromosome names are the same between your BAM and your GTF?

ADD REPLY • link 4.6 years ago by ATpoint 85k

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Chromosomes name of these two files are different.

enter link description here

ADD REPLY • link 4.6 years ago by baurumon ▴ 30

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There is your reason why nothing can be mapped.

ADD REPLY • link 4.6 years ago by ATpoint 85k

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