Entering edit mode
2.7 years ago
biology_inform
▴
50
Hi,
htseq-count -f bam -s yes ~/htseq-trial/SRR13826419_Aligned.sortedByName.out.bam ~refgen/gencode.v39.primary_assembly.annotation.gtf > counts.txt
I am trying to run htseq-count with command above but in the err file
[E::idx_find_and_load] Could not retrieve index file for '~/htseq-trial/SRR13826419_Aligned.sortedByName.out.bam'
100000 GFF lines processed.
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3241580 GFF lines processed.
[E::idx_find_and_load] Could not retrieve index file for '~/htseq-trial/SRR13826419_Aligned.sortedByName.out.bam'
100000 alignment record pairs processed.
200000 alignment record pairs processed.
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8767930 alignment record pairs processed.
So what should I do for that index file?
Yes, and for this you have to sort by coordinate. Make your life easy and use
featureCounts, it is faster and works on name-sorted files out of the box.I know featureCounts but my prof wants me to learn htseq besides featurecounts. Thanks again
I ran the same command but when I run the htseq;
the index should have extension
.bainormallybut can i use .bai file as an input for htseq-count?
Should they be in the same path, the .bai and .bam?
You should use the bam files as input and leave the index files in the same folder as the bam files.
Yes I just figured that out thanks again :))