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Question: Human RNA-Seq paired-end libraries
0
gravatar for ose140
3.5 years ago by
ose140 • 0
ose140 • 0 wrote:

Hello,

I would like to study and doing exersizes in RNA-seq analysis that are based on paired-end

libraries. In particular, I prefer to work with relatively small FASTQ files (otherwise each analysis

will take me a very long time).

According to several websites there should be  “Human RNA-Seq paired-end” shared data

library  in Galaxy (according to http://training.bioinformatics.ucdavis.edu/docs/2015/03/march-2015-workshop/Wednesday_MB_Tophat_PE.html). 

Unfortunately, I could not find this library in the shared data libraries of GALAXY. I would like

to ask please if somebody can give me a link to this library and/or other libraries of small

paired-end sequencing files.

Thank you in advance.

 
rna-seq • 935 views
ADD COMMENT • link •
modified 3.5 years ago by Martin Čech ♦♦ 4.9k • written 3.5 years ago by ose140 • 0
0
gravatar for Bjoern Gruening
3.5 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

I don't know about these datasets but please have a look at the Galaxy 101 tutorial which is currently rewritten and enhanced.
ADD COMMENT • link written 3.5 years ago by Bjoern Gruening ♦ 5.1k

Hi Bjoern Gruening,

Thank you for your answer. However, what I'm looking for are specific links for dataset files (FASTAQ)

from paired-end RNA sequencing that are not too big (not more than 200,000 reads) such that I can 

use them for a practice/training in RNA splicing analysis. All the files that I have found so far from 

GALAXY website, NCBI and EBI are too big (several GBs). It takes more than 20 hours to run each 

one of them. So, even little information about where I can find small paired-end sequencing files

will help me a lot.

Thank you

ADD REPLY • link written 3.5 years ago by ose140 • 0

What we are usually doing is extracting one chromosome. Maybe you can do the same?

ADD REPLY • link written 3.5 years ago by Bjoern Gruening ♦ 5.1k
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