error profile plot

nanto · 09-19-2012, 06:55 AM

I'm doing quality control of my alignments from bwa-sw. I would like to make a error profile plot for that, but samstat does not generate one (with comparision on insertions, deletions and so on). Also for long reads all the plots from samstat are not very readable.

Also I managed to get the graph of hits per contig from sam file via samtools, but I'm also interested if estimating to how many contigs particular read matches (from blast alignments it was even up to 100 contigs to which read was mapped) so I'm curious how does it look for bwa-sw alignment. Does any one have any python script for that?

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09-19-2012, 06:55 AM	#1
nanto Member Location: Wageningen, Netherlands Join Date: Sep 2012 Posts: 19	error profile plot I'm doing quality control of my alignments from bwa-sw. I would like to make a error profile plot for that, but samstat does not generate one (with comparision on insertions, deletions and so on). Also for long reads all the plots from samstat are not very readable. Also I managed to get the graph of hits per contig from sam file via samtools, but I'm also interested if estimating to how many contigs particular read matches (from blast alignments it was even up to 100 contigs to which read was mapped) so I'm curious how does it look for bwa-sw alignment. Does any one have any python script for that?