SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > SOLiD



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to extract multi-mapped reads by samtools? mavishou RNA Sequencing 5 12-05-2016 05:27 AM
Extract subset of Fastq sequences based on a list of IDs pepperoni Bioinformatics 36 05-06-2013 01:38 AM
Error Bowtie with fastq files (from Solid .csfasta & .qual) pepperoni Bioinformatics 0 10-12-2011 08:20 PM
Extract perfectly mapped reads from SAM/BAM file Graham Etherington Bioinformatics 2 07-21-2011 07:27 AM
fastq to csfasta and .qual samt SOLiD 15 10-29-2009 09:11 AM

Reply
 
Thread Tools
Old 01-18-2010, 12:30 AM   #1
KevinLam
Senior Member
 
Location: SEA

Join Date: Nov 2009
Posts: 199
Default extract subset (mapped reads) from csfasta and .qual files

Hi
Is there a ready script that extracts a subset of reads ( I wish to extract mapped reads) from csfasta?
Hopefully the same script will output a new csfasta file and new qual.

Cheers
Kevin
KevinLam is offline   Reply With Quote
Old 01-18-2010, 12:38 AM   #2
KevinLam
Senior Member
 
Location: SEA

Join Date: Nov 2009
Posts: 199
Default

it is kinda like a general question for
http://seqanswers.com/forums/showthread.php?p=12272

I would have used Bio::SeqIO except that I think it would be terribly slow plus its for fasta not csfasta.
basically I am looking for a index method of retrieving reads

any help appreciated!
KevinLam 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 11:07 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO