Short-reads in FASTA format

[CS Student]

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.

[Rocketknight]

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):

#!/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.

[CS Student]

Thanks a lot for your help. I found some tools to convert from FASTAQ to FASTA.