colour space fiiltering

paolo.kunder

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Join Date: Aug 2011

Posts: 93
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colour space fiiltering

03-28-2012, 11:05 PM

Dear All,
I downloaded and executet csfasta_quality_filter.pl script on my SOLiD 5500 csfasta (and qual) data to trim a fixed number of colors. ( code below)

perl csfasta_quality_filter.pl -f F5.cs fasta -q F5.QV.qual -o 5_bases_trimmed_F5.csfasta --num_colors_to_hard_trim 5

I was wondering about the output file, from the manual (Filtered and trimmed reads are output in csfasta format to a user-specified filename). And where is my associated QV.qual file trimmed? Any ideas? I cannot supply TopHat or any other alignment software with a trimmed csfasta and a full lenght associated quality file..

Any other script to trim colour space data?
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