Entering edit mode
4.7 years ago
fatimarasool135
▴
90
Hi. I have encountered error while working on htseq-count. I have studied this error on many form. The solution to this error was sort the bam file by name. I did same by using this command as
samtools sort -n myfile_align.bam -o myfile_sortedn.bam
then i run the comand on htseq as
htseq-count -f bam -r name -i gene_id -s no -t exon myfile_sortedn.bam reference.gtf > myfile_htseq_count.txt
I got the same wornings again after sorting as
Warning: Read NS500786:42:HW75GBGXX:1:11101:1523:3911 claims to have an aligned mate which could not be found in an adjacent line.
Warning: 1301378 reads with missing mate encountered.54666717 SAM alignment pairs processed.
Can you please tell me other solution to remove this warnings.
Some mates are missing. Did you filter the BAM file in any fashion? You can try
to remove the paired-end flag in case the read is a singleton.