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Old 03-28-2012, 11:05 PM   #1
Location: Milano, Italy

Join Date: Aug 2011
Posts: 93
Default colour space fiiltering

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

perl -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?
paolo.kunder is offline   Reply With Quote

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