Short-reads in FASTA format

CS Student · 03-13-2012, 10:42 AM

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 · 03-15-2012, 06:44 AM

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.

CS Student · 03-15-2012, 11:39 AM

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

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03-13-2012, 10:42 AM	#1
CS Student Member Location: US Join Date: Apr 2011 Posts: 20	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.

03-15-2012, 06:44 AM	#2
Rocketknight Member 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): 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.

03-15-2012, 11:39 AM	#3
CS Student Member Location: US Join Date: Apr 2011 Posts: 20	Thanks a lot for your help. I found some tools to convert from FASTAQ to FASTA.