Hi, I am really new to bioinformatics so please help me figure out this error. I have tried looking at other threads with similar questions but couldn't resolve my problem.
I get the following error when I am using HTseq for counting:
Error occured when reading beginning of SAM/BAM file. ('SAM line does not contain at least 11 tab-delimited fields.', 'line 1 of file Sorted_KKUGCTM5_-VE_14-4_aligned.bam') [Exception type: ValueError, raised in _HTSeq.pyx:1276]
The code I am using is as follows:
/HTSeq-0.6.1/scripts/htseq-count --stranded=no Sorted_KKUGCTM5_-VE_14-4_aligned.bam GRCh38/Homo_sapiens.GRCh38.90.gtf
I have tried using the above code, then I also tried converting the above bam file to sam file, and then used the sam file in the above-mentioned code, and I still get the following error:
Warning: Malformed SAM line: MRNM != '*' although flag bit &0x0008 set Warning: Read 700463F:369:CB93CANXX:5:1103:15415:8299 claims to have an aligned mate which could not be found in an adjacent line. Error occured when processing SAM input (line 57 of file Sorted_KKUGCTM5_-VE_14-4_aligned1.sam): 'pair_alignments' needs a sequence of paired-end alignments [Exception type: ValueError, raised in __init__.py:603]
Please help where am I going wrong?