Actually I have several questions to ask but I try to be very much to the point.
I want to upload data from ftp ebi.ac.uk) into galaxy and then align them by HISAT2 and then extract the htseq-count.
Simply I long in into galaxy, then I click on https://www.ebi.ac.uk/ena/data/ 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 ebi.ac.uk why is that ? 2- can someone show how to use HISAT2 in this case ? 3- how to get the hsetq-count ?