SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
fastq-dump on SRA files harlock0083 Bioinformatics 14 10-18-2018 03:19 AM
fastq-dump error erikm Bioinformatics 10 03-24-2016 04:23 AM
SRA to fastq conversion with fastq-dump loses sequences pcantalupo Bioinformatics 13 10-08-2015 04:09 PM
fastq-dump runs indefinitely on windows Zergling RNA Sequencing 0 09-07-2011 08:25 PM
fastq-dump for Illumina duygu Bioinformatics 3 08-03-2011 02:00 PM

Reply
 
Thread Tools
Old 06-10-2011, 03:40 AM   #1
Giles
Member
 
Location: Birmingham, Al

Join Date: Feb 2010
Posts: 39
Default Fastq-dump.exe

Has anybody gotten this to work using windows? If not, are there any ways to convert sra to fastq for someone on a windows OS? It seems that Galaxy has nothing regarding sra file formats.
Giles is offline   Reply With Quote
Old 06-10-2011, 04:00 AM   #2
Giles
Member
 
Location: Birmingham, Al

Join Date: Feb 2010
Posts: 39
Default I think I got it

I went back to NCBI website and found a ncbi sra toolkit designed for 32 bit windows os. It seems to be working now.
Giles is offline   Reply With Quote
Old 06-11-2011, 12:34 PM   #3
tnabtaf
Member
 
Location: Oregon

Join Date: Jan 2011
Posts: 53
Default Use SRA to do conversion?

A few months ago Stephen Taylor suggested using the SRA's conversion itself:
The way I got round this was let the SRA website do the conversion. So just paste in the URL in the upload screen:

http://trace.ncbi.nlm.nih.gov/Traces...X&format=fastq

Where SRRXXXXXX is the archive of interest, and it downloads Sanger FASTQ sequences to Galaxy.
tnabtaf is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:40 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO