Question: MeDIP-seq and hMeDIP-seq analysis
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gravatar for Grinch
5.1 years ago by
Grinch90
Germany
Grinch90 wrote:

Hi! I'm analysing MeDIP-seq and hMeDIP-seq data for the first time (I've analysed ChIP-seq and RNA-seq data sets before) and was wondering if people who have done it before can recommend pipelines they have used and/or programmes for quantitative comparison of ChIP-Seq data. My data set is made of replicates and has 2 disease subtypes and healthy samples.

I've analysed with the new MethylAction pipeline and MACS peak caller, but to compare between the two I need to choose a programme for quantitative comparison for the peaks I get with MACS, so I can see which one gives me better results for my data.

If anyone has knowledge of a better pipeline, that would also be of use, but firstly I need to quantitate the peaks.

Thank you all!

chip-seq hmedip-seq medip-seq • 2.7k views
ADD COMMENTlink modified 5.1 years ago by dally190 • written 5.1 years ago by Grinch90
1
gravatar for dally
5.1 years ago by
dally190
United States
dally190 wrote:

https://ethanomics.wordpress.com/2014/02/19/medip-seq-data-analysis-diffreps/

This might at least get you looking in the right direction. I've used diffReps before and it's quite easy to work with.

ADD COMMENTlink written 5.1 years ago by dally190

Hello, I'm using diffReps to analyse hMeDIP -seq data without replicate . I enter the command of "diffReps.pl --treatment 3dr_q20_peaks.broadPeak --control 3dl_q20_peaks.broadPeak --report ./diffReps/diff_chip3d_peak --chrlen genome_length.txt --meth gt &". But I get the error "Cannot delete file .1604405765.13726.chrY.bed: No such file or directory" or so so much . I put three bed files and chrlen file in one folder. Cound you help me analyse it ?

ADD REPLYlink written 3 months ago by 15150980450

/home/syd/miniconda3/envs/chipseq/bin/diffReps.pl --treatment 3dR_cutadapt_trim1010.aln.q20.bed --control 3dL_cutadapt_trim1010.aln.q20.bed --report diff_chip3d --chrlen genome_length.txt --btr 3d_input_cutadapt_trim10.aln.q20.bed --bco 3d_input_cutadapt_trim10.aln.q20.bed --meth gt --nproc 4

I get bed files from bam files by bedtools.

ADD REPLYlink written 3 months ago by 15150980450
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