I have downloaded a few tissue bam files from illumina body map from the link
Now to get the read counts from each of the tissue sample bam files, I did HTSeq analysis. But unfortunately for a few tissues it worked really well but for a few tissues it ended up showing different error each time I run HTSeq analysis.
The HTSeq command I am using for processing bam files is
samtools view GRCh38.illumina.ovary.1.bam | htseq-count -i gene_id - Homo_sapiens.GRCh38.80.gtf > htseq.ovary.results.txt
shows an error of
Error occured when processing SAM input (line 2):
'pair_alignments' needs a sequence of paired-end alignments
[Exception type: ValueError, raised in __init__.py:603]
I tried sorting the sam files too, but still it dint work :( showed some error
Error occured when reading beginning of SAM/BAM file.
[Exception type: StopIteration, raised in count.py:88]
How to solve this issue pleaseeeeeee help someone!