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Old 03-13-2012, 09:42 AM   #1
CS Student
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Location: US

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

Hi,

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?

Thanks.
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Old 03-15-2012, 05:44 AM   #2
Rocketknight
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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):
Code:
#!/usr/bin/python
import re, sys

try:
    filename = sys.argv[1]
except:
    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.
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Old 03-15-2012, 10:39 AM   #3
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Thanks a lot for your help. I found some tools to convert from FASTAQ to FASTA.
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