Question: how to perform alignment using Hisat2
gravatar for Learner
9 months ago by
Learner 10
Learner 10 wrote:

Actually I have several questions to ask but I try to be very much to the point.

I want to upload data from ftp into galaxy and then align them by HISAT2 and then extract the htseq-count.

Simply I long in into galaxy, then I click on and then search for one job and click one by one on the FASTQ files (Galaxy) and it will import them to my workspace. Now the questions

1- I get two fastq files for each sample using why is that ? 2- can someone show how to use HISAT2 in this case ? 3- how to get the hsetq-count ?


rna-seq alignment • 589 views
ADD COMMENTlink modified 9 months ago by Jennifer Hillman Jackson25k • written 9 months ago by Learner 10
gravatar for Jennifer Hillman Jackson
9 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Please see the RNA-seq tutorials here for example workflows:

Thanks! Jen, Galaxy team

ADD COMMENTlink written 9 months ago by Jennifer Hillman Jackson25k
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