Hi all- I have been trying to figure this out for hours but not getting anywhere. Any suggestion is greatly appreciated!

I am trying to use htseq-count to get raw count from an alignment file, myAlignedFile.bam, output from gsnap.

Then I name-sorted the bam file, converted to sam, and run htseq-count:

samtools sort -n myAlignedFile.bam myAlignedFile_nsorted
samtools view myAlignedFile_nsorted.bam>myAlignedFile_nsorted.sam
python -m HTSeq.scripts.count -m intersection-strict myAlignedFile_nsorted.sam genes.gtf > htseq_count_result.txt

However, I got thousands of warnings like this:

Warning: Read HWI-ST845:130320:D20JBACXX:8:1101:6938:66256 claims to have an aligned mate which could not be found. (Is the SAM file
properly sorted?)

I was still able to get counts in the output file; however, I'm worried that I did something wrong and the result is not reliable. Any idea what I did wrong during these processes?

Many thanks in advance!