Go Back   SEQanswers > General

Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA using reads in FASTA format aggp11 RNA Sequencing 7 08-11-2012 06:55 PM
Align multiple sequences in tabular or fasta format pchiang Bioinformatics 7 07-01-2011 11:18 PM
help needed to retrieve fasta reads from fasta db prashanthpnu Bioinformatics 1 06-21-2011 06:59 AM
Where can I find the complete FASTA format sequence(human and mouse)? iloveneworleans Bioinformatics 5 02-24-2010 05:00 PM
newbler assembly of mated reads (FASTA format) dpuiu De novo discovery 1 01-22-2010 12:27 AM

Thread Tools
Old 03-13-2012, 10:42 AM   #1
CS Student
Location: US

Join Date: Apr 2011
Posts: 20
Default Short-reads in FASTA format


I need to run some experiments on short-reads in fasta format. However, all the sources I found is using FASTAQ format for short-reads. I tried some tools for converting FASTAQ to FASTA, but still having problems with the converted files.

Could you please point me to sources where I can download short-reads (small files for testing purposes only) in fasta format?

CS Student is offline   Reply With Quote
Old 03-15-2012, 06:44 AM   #2
Location: Ireland

Join Date: Sep 2011
Posts: 86

Very few places will have those available, as almost all aligners are designed to work with FASTQ data, and all modern short-read sequencers only output FASTQ. However, since I assume you're just trying out your own alignment programs, this short python script I whipped up should convert FASTQ to FASTA pretty easily (run it with an input FASTQ file as an argument, make sure the file isn't gzipped first):
import re, sys

    filename = sys.argv[1]
    exit('Need to supply an input file!')

f = open(filename)
counter = 0
for line in f:
    counter = 1 if counter == 4 else counter+1
    if counter == 1:
        print '>'+re.sub(r'>','',line)[1:].rstrip()
    elif counter == 2:
        print line.rstrip()
If for whatever reason this isn't working for you, let me know and I'll run it on one of my FASTQ files here and e-mail you the result.
Rocketknight is offline   Reply With Quote
Old 03-15-2012, 11:39 AM   #3
CS Student
Location: US

Join Date: Apr 2011
Posts: 20

Thanks a lot for your help. I found some tools to convert from FASTAQ to FASTA.
CS Student is offline   Reply With Quote

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 12:52 PM.

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