Hi,
I tried to extract only those reads from a SAM file that mapped to larger scaffolds. I did this with
>grep -f list_of_large_scfs.txt alignment.sorted.sam > aln.large_scfs.sam
I wanted to parse the output file to cufflinks, but I keep getting the error that the file isn't sorted correctly, even if I sort them with sort -k 3,3 -k 4,4n.
Does anyone know what could be happening here?
I tried to extract only those reads from a SAM file that mapped to larger scaffolds. I did this with
>grep -f list_of_large_scfs.txt alignment.sorted.sam > aln.large_scfs.sam
I wanted to parse the output file to cufflinks, but I keep getting the error that the file isn't sorted correctly, even if I sort them with sort -k 3,3 -k 4,4n.
Does anyone know what could be happening here?
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