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Old 12-15-2010, 04:04 AM   #1
mucku
Member
 
Location: Berlin

Join Date: Jan 2009
Posts: 14
Question Splitting fasta AND quality on masked sequence

Hello,
does anybody have a script or any program that allows me to split fasta sequences and the according quality file on masked bases such as "N"? Everything I find works perfectly on fasta files but the quality files are never touched. I think even FastQ format would be ok because conversion is easy these days using Galaxy.

Any help would be appreciated.

Cheers,

Markus

Example:

>fasta
GACTAGCGATCGACGATCGNNNNNNGACGAGCGACGAGCGA
>qual
20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 10 10 10 10 10 10 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20

>fasta_new1
GACTAGCGATCGACGATCG
>fasta_new2
GACGAGCGACGAGCGA
>qual_new1
20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
>qual_new2
20 20 20 20 20 20 20 20 20 20 20 20 20 20 20 20
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