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Old 09-08-2015, 04:26 AM   #1
Saeideh
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Location: Iran

Join Date: Aug 2015
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Default Where can I find sequence reads?

Hi~~

Where can I download sequence reads directly? (without installing applications; like ftp)

I want small cDNA reads to test TopHat and cufflinks fast. I tried to design a file with a few reads but because there is bias, the quality of my reads are so low.

Thank you..
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Old 09-08-2015, 09:03 AM   #2
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

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Most web browsers offer direct FTP support via:

ftp://usernameassword@ftp.xyz.com

I realize that you are in Iran and thus may have a more limited web browser but I suggest trying out your web browser first before writing off FTP

As for where to get the reads, I suggest the SRA at NCBI but it does depend on what organism you want. NCBI does like to use Aspera as a download method but you should be able to step around that.
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Old 09-08-2015, 09:59 AM   #3
GenoMax
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@Saeideh: If you are unable to use the download methods then try "randomreads.sh" program from BBMap suite. You can provide it a fasta reference to generate random reads with characteristics you can control: http://seqanswers.com/forums/showthread.php?t=48988
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