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Error using htseq-count: Could not retrieve index file
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+ Bioinformatics
+ Rna-seq
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Mustafa Direk
Error using htseq-count: Could not retrieve index file
The problem seems to be missing index files of the bam files (therefore the error message that the index file is missing). You should be able to generate those with samtools, e.g.
samtools index ./OVCA429_587680_1_1.rnaseq.fastqAligned.sortedByCoord.out.bam
The problem seems to be missing index files of the bam files (therefore the error message that the index file is missing). You should be able to generate those with samtools, e.g.
samtools index ./OVCA429_587680_1_1.rnaseq.fastqAligned.sortedByCoord.out.bam
As it happens I did have the index file as well, I just ended up naming it differently and so the application probably didn't recognise it. Once I changed the name to match the bam file, it worked out perfectly file. Nevertheless, thank you for your help! :)More
The problem seems to be missing index files of the bam files (therefore the error message that the index file is missing). You should be able to generate those with
samtools, e.g.The problem seems to be missing index files of the bam files (therefore the error message that the index file is missing). You should be able to generate those with
samtools, e.g.More
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