SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
NGS whole genome sequence versus sequence capture for quality control houkto Bioinformatics 0 02-02-2012 05:16 AM
Annotating FASTA sequence gokhulkrishnakilaru Bioinformatics 3 10-13-2011 12:40 PM
bwa masked sequence? rand Bioinformatics 2 11-09-2009 07:02 AM
why consed finds discrepancies with masked n sequence alig Illumina/Solexa 3 06-12-2009 01:32 PM
a question about fasta quality. cgjkjk Bioinformatics 0 12-17-2008 09:34 AM

Reply
 
Thread Tools
Old 12-15-2010, 05:04 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
mucku is offline   Reply With Quote
Old 12-15-2010, 07:11 AM   #2
drio
Senior Member
 
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

I don't think you'll find any tool. Sounds like is time to put your scripting skills to work ?
__________________
-drd
drio is offline   Reply With Quote
Old 12-15-2010, 07:16 AM   #3
colindaven
Senior Member
 
Location: Germany

Join Date: Oct 2008
Posts: 415
Default

You can convert to fastQ using a perl script helpfully provided in these forums - I've done this in the past, you'll have to search for it. Then as you say manipulation is easier.
colindaven is offline   Reply With Quote
Old 12-15-2010, 12:53 PM   #4
mucku
Member
 
Location: Berlin

Join Date: Jan 2009
Posts: 14
Default

My scripting skills are the problem... I know some basic shell stuff like grep, sed, awk etc. I come more from the wetlab. Using pre-existing tools and some mild reformatting is ok for me. But I am not sure how to approach this...
I am still trying to learn some biopython in my spare time...
mucku 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 11:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO