Fastq file to ALN file

Question

[bdeonovic]

I have a fastq file (CHIP-seq) and I would like to use cisGenome for my analysis. It requires an ALN file:

The file should be tab-delimited and should have three columns as follows:

chr1[tab]359077[tab]F
chr1[tab]376890[tab]R
....

This is called ALN format. A file in this format usually has a name ending with *.aln.

What is the recommended way of getting fastq to aln? aln

For my own reference:

• Guide to Peak Calling
• 2009 CHiP-seq Review
• 2010 CHiP-seq algo Review

Answer 1

[Devon Ryan]

You'll need to align the reads to the genome first (bowtie2 and BWA are popular aligners for this purpose). Then you can use awk on the resulting file. BTW, it's usually a sign that a package is no longer maintained when it doesn't natively support SAM/BAM files.

[bdeonovic]

Do you have a recommendation for software that does histone methylation analysis for CHIP-seq?

[Devon Ryan]

For which step(s)? I'm guessing that you're new to this, so your life will be easier if you can either find a local collaborator to help you through the first analysis or take a course (I don't have any links handy, unfortunately, but you should be able to find one with a bit of googling).

[bdeonovic]

Yes, new. My PI gave me data and told me to use cisGenome. He also talked about MACS, but suggested that MACS was better for dealing with transcription factor analysis.

[Devon Ryan]

Perhaps cisGenome has an alignment feature, I've never used it. If nothing else, just align with one of the aforementioned aligners and then convert the resulting SAM file to that format with awk (go ahead an post again once you have your SAM or BAM files and need help doing the conversion). I would strongly encourage you to read some recent review articles on peak calling. The unfortunate reality is that most PIs are flying pretty blind with this sort of thing, so there may be some better options for your dataset.

[bdeonovic]

Thanks, I'll take a look. I posted some helpful review articles for anyone in the future who is interested.