Question: Align FastQ file to reference mouse mm9 genome
gravatar for tanni93
4.5 years ago by
United States
tanni9310 wrote:

Hi all,

I am new to chip-seq analysis. I am using Bowtie to align one fastQ file to reference genome. Do I do alignment one file at a time or can I run all 9 files at the same time? I found this useful page: but I would like to know where they are actually writing their commands/promts --> terminal in mac? 

Any help is greatly appreciated!

Thank you,
Tanni Arif 


rna-seq • 1.6k views
ADD COMMENTlink modified 4.5 years ago by genomax83k • written 4.5 years ago by tanni9310

This is probably unpopular opinion since most people here are very advanced in this sort of thing. But coming from a primarily wetlab background and only about a month of bioinformatic work, I started off by aligning my fastq files one at a time. Sure it's slow, but you learn quite a bit.

Yes they bowtie uses the terminal to write commands.

EDIT: Misunderstood, you should definitely merge all fastq files before running.

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.5 years ago by Bioradical60

Thank you all!

ADD REPLYlink written 4.5 years ago by tanni9310
gravatar for TriS
4.5 years ago by
United States, Buffalo
TriS4.2k wrote:

if the files are all from the same experiment/replicate/condition you can concatenate your fastq files and then run bowtie.

not sure how big are your files but running bowtie locally (i.e. your mac) is not the best idea. normally these analysis, being VERY computationally expensive, are run on a UNIX server that has lots or memory and a number or CPUs available (although your mac should have multiple cores depending from when you got it).

check with your IT department to make sure you can have access to it.

ADD COMMENTlink written 4.5 years ago by TriS4.2k
gravatar for genomax
4.5 years ago by
United States
genomax83k wrote:

Before you worry about the alignments it sounds to me like you should spend a couple of hours learning about basics of unix here. Once you become somewhat familiar with the command line, implementing solutions found here and on SeqAnswers will be (relatively) easy.

ADD COMMENTlink modified 4.5 years ago • written 4.5 years ago by genomax83k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 821 users visited in the last hour