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Old 09-13-2011, 02:27 AM   #1
ramashankar16
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Default SRA to FASTQ

hi folks i have to do the transcriptome analysis using illumina sequencing so could you please tell me ho to convert the sra file into fastQ formate
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Old 09-13-2011, 02:34 AM   #2
ulz_peter
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You should think about moving your question somewhere else, as the topic is by no means related to your question...
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Old 09-13-2011, 05:26 PM   #3
nilshomer
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Quote:
Originally Posted by ulz_peter View Post
You should think about moving your question somewhere else, as the topic is by no means related to your question...
Moved, good catch.
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Old 09-13-2011, 05:58 PM   #4
masylichu
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fastq-dump

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Originally Posted by ramashankar16 View Post
hi folks i have to do the transcriptome analysis using illumina sequencing so could you please tell me ho to convert the sra file into fastQ formate
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Old 09-13-2011, 06:31 PM   #5
robs
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The mentioned program is part of the SRA Toolkit and can be found here:
http://trace.ncbi.nlm.nih.gov/Traces...are&s=software

Help on how to use the fastq-dump can be found here:
http://www.ncbi.nlm.nih.gov/books/NB...erting_SRA_for

Good luck!
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Old 10-26-2011, 03:03 AM   #6
seenstevo
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Hi there. I have been using the SRA toolkit and have had no trouble using the fastq-dump tool but I have also been trying to get the SRA files into SFF format to use sff_extract for use with MIRA3 assembler. Unfortunately I can't get it to work and as a complete novice (both with bioinformatics and LINUX) working more or less alone on this I would really appreciate any help if anyone has used it. Any alternate approaches would also be appreciated for assebling and analysis of 454 EST data.
Thanks, seenstevo
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