SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Stupid perl scripts for converting colour-space <-> base-space gringer Bioinformatics 7 07-20-2011 07:35 AM
Human transcriptome reference in colour space hbt Bioinformatics 0 07-06-2011 06:04 AM
Converting nucleotide-space to color-space javijevi Bioinformatics 7 11-29-2010 02:14 AM
Solid formats translator(base space/color space/double encoded) AronaldJ SOLiD 0 10-26-2010 12:10 AM

Reply
 
Thread Tools
Old 03-28-2012, 11:05 PM   #1
paolo.kunder
Member
 
Location: Milano, Italy

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

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?
paolo.kunder is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:17 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO