Question: Fastq file to ALN file
gravatar for bdeonovic
6.1 years ago by
United States
bdeonovic180 wrote:

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:






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

cisgenome chip-seq fastq aln • 2.3k views
ADD COMMENTlink modified 6.1 years ago • written 6.1 years ago by bdeonovic180
gravatar for Devon Ryan
6.1 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

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 BTW, it's usually a sign that a package is no longer maintained when it doesn't natively support SAM/BAM files.

ADD COMMENTlink written 6.1 years ago by Devon Ryan96k

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

ADD REPLYlink written 6.1 years ago by bdeonovic180

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).

ADD REPLYlink written 6.1 years ago by Devon Ryan96k

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. 

ADD REPLYlink written 6.1 years ago by bdeonovic180

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.

ADD REPLYlink written 6.1 years ago by Devon Ryan96k

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

ADD REPLYlink written 6.1 years ago by bdeonovic180
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