SRA to FASTQ

[ramashankar16]

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

[ulz_peter]

You should think about moving your question somewhere else, as the topic is by no means related to your question...

[nilshomer]

You should think about moving your question somewhere else, as the topic is by no means related to your question...

Moved, good catch.

[masylichu]

fastq-dump

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

[robs]

The mentioned program is part of the SRA Toolkit and can be found here:

http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software

Help on how to use the fastq-dump can be found here:

http://www.ncbi.nlm.nih.gov/books/NBK47540/#SRA_Download_Guid_B.5_Converting_SRA_for

Good luck!

[seenstevo]

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