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Old 09-16-2010, 07:22 AM   #1
A1_UltiMA
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Default BLASTing or Convert FASTQ: any user-interface programmes out there? Need help!

BlastStation-Free, acts as a standalone BLAST program which has a user interface rather than having to use command lines: problem is, is that it only accepts FASTA, and not FASTQ.

We could either:

1. Find a new standalone user-interface BLAST program that accepts FASTQ.

or

2. Find a FASTQ to FASTA converter with a user-interface.

Does anybody have suggestions of either of the programmes we need?

Thankyou for reading.
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Old 09-16-2010, 07:55 AM   #2
sdarko
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Galaxy (http://main.g2.bx.psu.edu/) is web based and has a FASTQ to FASTA converter. You might want to try that.

Sam
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Old 09-16-2010, 08:23 AM   #3
A1_UltiMA
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Hey Sam,

Thanks very much, you're right, but actually there is simply too much data to upload; around 80GB.
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Old 09-16-2010, 08:36 AM   #4
sdarko
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Possibly try this program --> http://sourceforge.net/projects/ngssequencealig/files/
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Old 09-17-2010, 04:08 AM   #5
maubp
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EMBOSS seqret can do FASTQ to FASTA (command line interface).
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Old 09-17-2010, 04:35 AM   #6
NicoBxl
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use awk !

awk 'BEGIN{P=1}{if(P==1||P==2){gsub(/^[@]/,">");print}; if(P==4)P=0; P++}' input.fastq > output.fasta


very easy
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Old 09-17-2010, 09:16 PM   #7
malachig
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Same idea using Perl

perl -ne '$c++; if ($c==1){$_=~/\@(\S+)/; print ">$1\n"} if($c==2){print "$_"} if ($c==4){$c=0}' input.fastq > output.fasta

Or if you find yourself wanting to manipulate fastq files in additional ways, the fastq utilities of Galaxy that sdarko mentioned above are available in command line form within the FASTX-Toolkit

Last edited by malachig; 09-17-2010 at 09:20 PM.
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