Galaxy NGS Tutorial (Stuck at a point)

Question

[pablosolar.r]

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

Answer 1

[Michael]

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.

Answer 2

[pablosolar.r]

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?

[Devon Ryan]

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.