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7.8 years ago
jleandroj
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0
In a sam file I have MAPQ (mapping quality) for each read. Is there an equivalent or similar to MAPQ in a psl file? if not, what can measure I can use to select the best quality of reads in a psl file. I am trying to do it without samtools (using only awk or grep).
Did the psl file come from a
blatsearch?yes, it is. I did with pblat.
There isn't an equivalent value in blat psl files that you can use.
Thanks for helping me.
Yes, it seems be that there is not equivalent but in other forums. people suggested to take a look in the first column. Moreover, some professors said that matches( first column of psl file) is the closest parameter to quality in this file.