Question: SICER raw data
0
gravatar for chipseq33
4.3 years ago by
chipseq3310
chipseq3310 wrote:

Hi,

I am trying to use SICER on my H3K27me3 data. has anybody experience with this software? does it use the fastq files for mapping?

I had a look at the manual but I did not get how I should run it ? what this means "raw data need to be in the BED"?

may be I am asking too much, but, could you please share your script for running SICER for H3K27me3?

Thank you for your help

chipseq • 1.7k views
ADD COMMENTlink modified 4.3 years ago by dariober11k • written 4.3 years ago by chipseq3310
6
gravatar for dariober
4.3 years ago by
dariober11k
WCIP | Glasgow | UK
dariober11k wrote:

For the record if anybody is interested, just yesterday I started re-writing a wrapper around the SICER pipeline. The package is here https://github.com/dariober/SICERpy. Among other things, I make sicer accept bam files rather then bed.

I started using SICER and it gives sensible results but the user interface is a bit frustrating...!

ADD COMMENTlink written 4.3 years ago by dariober11k

That looks like a big step forward, I hope the original authors incorporate this!

ADD REPLYlink written 4.3 years ago by Devon Ryan96k
3

Great work! Do not work too hard on it though, I have an all parallel numpy/scipy version coming out that uses minutes where SICER used hours (or did not work at all) which is much easier to use ;). Complete rewrite! I have had it lying around for a year, tweaking it. Now that I have spilled the beans I finally am commited to releasing the preprint (will do so within April 14).

Edit: not to diminish your work or anything, just felt bad not letting you know.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by endrebak830

Great, looking forward to that and thanks for the heads up! I thought someone MUST have done something... Sicer is still very popular, the encode project used it but it's really messy and inefficient. Keep us posted!

ADD REPLYlink written 4.3 years ago by dariober11k
1

https://github.com/endrebak/epic or epic: new ChIP-Seq caller based on the SICER algorithm

Please try it and report any issues (I'm the only one who has used it so bound to be some)

Thanks for making that script, I'm not sure whether epic would ever have been released if not for sicerpy.

ADD REPLYlink modified 4.3 years ago • written 4.3 years ago by endrebak830
1

Cool, thanks man! I'll give it a go...

I'm not sure whether epic would ever have been released if not for sicerpy

Yeah, I think I know that feeling I've got this piece of code that looks ok... but who cares?!... Well... some people do!

ADD REPLYlink written 4.3 years ago by dariober11k

Come to think of it, SICERpy is incredibly valuable. There is loads of functionality that exists in SICER that I do not intend to implement. Thanks for the script!

ADD REPLYlink written 4.3 years ago by endrebak830
1
gravatar for Devon Ryan
4.3 years ago by
Devon Ryan96k
Freiburg, Germany
Devon Ryan96k wrote:

You'll need to align your fastq files with whatever aligner you prefer (e.g., bowtie2, or bwa) and then convert the resulting SAM or BAM file into a BED file (yes, this seems incredibly silly). Bedtools has a bamtobed command that can facilitate this last step.

ADD COMMENTlink written 4.3 years ago by Devon Ryan96k
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