Hi everyone,
I am very, very new to the bioinformatics field. I have been tasked with what seems like an insurmountable job, of taking publicly available ChIP-seq data sets, mapping them, and overlaying the peak locations.
They are all different types of files, and I have no idea where to start.
I am not asking to be spoon fed information, I would just like to know a workflow, as in where do I start and how do I progress?
Any help will be very much appreciated!
There are several resources online (google?). These two should get you going
http://www.biologie.ens.fr/~mthomas/other/chip-seq-training
http://www.nature.com/nprot/journal/v7/n1/full/nprot.2011.420.html
Thanks, this was really helpful!
I have come across a problem though. My code for bowtie doesn't seem to be working...
bowtie index=mm8.1.ebwt -q SRR1514105.fastq -v 2 -m 1 -3 1 -S 2> SRR1514105.out > SRR1514105.sam
shoots me back a message saying
Error: unexpected symbol in "bowtie index"
When I remove "index" I get a similar message.
Secondly, I am struggling to understand how to load up MACS. The instructions provided with it are rather cryptic. I feel way out of my depth!
bowtie -v 2 -m 1 -3 1 -q -S mm8 SRR1514105.fastq 2> SRR1514105.out > SRR1514105.sam
Regarding MACS (I presume MACS2), I'm not sure what you mean by "load" in this context. If you have it installed then you just run it (use the callpeak subcommand).
pip install --user macs2
Since you appear to be generally new to using the command line, you might also find "bioconda" to be useful. There, we present a single method to install most common bioinformatics packages.
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This workflow seems a nice starting point: NGS data analysis with R / Bioconductor: ChIP-Seq workflow