Question: Galaxy NGS Tutorial (Stuck at a point)
0
gravatar for pablosolar.r
3.6 years ago by
pablosolar.r20
pablosolar.r20 wrote:

Hi all!

I'm newbie in NGS and I'm trying to do this practical workshop from Galaxy (and trying to understand it):

http://ngsworkshop.aertslab.org/webpage/galaxy-rna-seq-workshop-2012.html

Point is that in step 4, there's no NGS: QC and manipulation -> Fastqc: Fastqc QC using FastQC from Babraham option in Galaxy.

So, what should I do to continue? Furthermore, If I had any kind of result at this point, the workshop says:

"Look at the result do you need to trim some bp due to low quality? If yes how many?"

How can I now how many? Could you help me?

Thank you in advance

rna-seq workshop quality galaxy ngs • 1.3k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by pablosolar.r20
0
gravatar for Michael Dondrup
3.6 years ago by
Bergen, Norway
Michael Dondrup47k wrote:

This page is pointing at an old workshop from 2012, you should try to find more recent materials. The workshop is pointing to a dysfunct galaxy instance. I guess you are using usegalaxy.org, this instance has FastQC under NGS: QC and manipulation.

ADD COMMENTlink written 3.6 years ago by Michael Dondrup47k
0
gravatar for pablosolar.r
3.6 years ago by
pablosolar.r20
pablosolar.r20 wrote:

Yes, but it's part of a practice from my Master estudies. I'll try with the one you said. I guess I should work with FASTQ files and not with the files generated with Clip adapter sequences tools, shouldn't I?

ADD COMMENTlink written 3.6 years ago by pablosolar.r20

Correct, the untrimmed fastq files will be rather more interesting in FastQC. BTW, there's a Galaxy conference with training at the end of June (Galaxy Community Conference 2016). Perhaps you might want to attend for some training.

ADD REPLYlink written 3.6 years ago by Devon Ryan93k
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