MeDIP-seq and hMeDIP-seq analysis

Question

[Fluorine]

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!

Answer 1

[dally]

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.

[1515098045]

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 ?

[1515098045]

/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.