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Fastq file to ALN file

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:

chip-seq aln cisgenome fastq
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updated by Ram Ram • written by bdeonovic bdeonovic

1 answer

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 BTW, it's usually a sign that a package is no longer maintained when it doesn't natively support SAM/BAM files.

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written by Devon Ryan Devon Ryan

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

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updated by Ram Ram • written by bdeonovic bdeonovic

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).

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updated by Ram Ram • written by Devon Ryan Devon Ryan

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.

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updated by Ram Ram • written by bdeonovic bdeonovic

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.

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written by Devon Ryan Devon Ryan

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

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updated by Ram Ram • written by bdeonovic bdeonovic

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