Dear All,
I am trying to use hisat2 program with cygwin on windows to align RNA seq reads. i am very new to this field and need some basic information how to run hisat2 from cygwin and then how to align the reads from my fastq files. Can you give some simple command lines with explanations, as i am completely blank in this field.
Are you sure you want to use cygwin? A simpler option will be to grab a linux based machine. If that does not work, you could set up a virtual linux machine on your windows PC. This can be of help:
https://dwheelerau.com/2014/07/25/install-arch-linux-on-virtualbox-the-nuts-and-bolts-pt1/
Once you are on linux, you will find tonnes of material that could be of help. Does not matter whether your aligner is HISAT2 or STAR or any other. You could look at the following paper:
http://www.nature.com/nmeth/journal/v14/n2/full/nmeth.4106.html
What Virag wrote is completely true. You could go for the Ubuntu or Biolinux as well.
Here is some help to get the package in Ubuntu:
https://www.thelinuxfaq.com/ubuntu/ubuntu-17-04-zesty-zapus/hisat2
Using cygwin for this work is not appropriate. Ubuntu is best option however, you can use biolinux which provides most of the tools pre-installed.
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