Thread: HTseq
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Old 09-06-2012, 05:18 AM   #1
narges
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Location: Finland

Join Date: Aug 2012
Posts: 29
Default HTseq

Hi all,
I have a BAM file from paired end tophat output and and I wanted to apply HTseq to count the mapped reads, because it was paired mate and also BAM, I did following steps but still I receive error:

samtools sort accepted_hits.bam accepted_hits.sorted

samtools view accepted_hits.sorted.bam | htseq-count - /hg19/Annotation/Genes/genes.gtf > count.txt

and this is the error :
Warning: Read ERR009097.6031922 claims to have an aligned mate which could not be found. (Is the SAM file properly sorted?)

Actually it was the same error I got before sorting so I did sorting but it is still the case.
And according to fastqc analysis for the left and right fastq files I have the same number of sequences.

Thanks for the help

Last edited by narges; 09-06-2012 at 05:39 AM.
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