Hello guys and gals!
I have a bit of a problem with samtools Sam-bam conversion. I have 8 files containing single read illumina data that I have aligned to my reference genome using bwa samse. No problems. Upon conversion, however, 4 out of 8 Sam files create a problem. The other 4 convert without a hitch.
I am writing this from my mobile so cannot copy in the error message, but it is the same that has been discussed here before - samtools complains about the sequence and quality information not matching and aborts.
Funnily, this only happens in the very last line of each Sam file! So I figured I just remove it and try again.
Any ideas as to how to accomplish this? I have tried opening the file in a simple text editor, but they are too massive (15GB)...
I have a bit of a problem with samtools Sam-bam conversion. I have 8 files containing single read illumina data that I have aligned to my reference genome using bwa samse. No problems. Upon conversion, however, 4 out of 8 Sam files create a problem. The other 4 convert without a hitch.
I am writing this from my mobile so cannot copy in the error message, but it is the same that has been discussed here before - samtools complains about the sequence and quality information not matching and aborts.
Funnily, this only happens in the very last line of each Sam file! So I figured I just remove it and try again.
Any ideas as to how to accomplish this? I have tried opening the file in a simple text editor, but they are too massive (15GB)...
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