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Old 02-21-2017, 03:46 AM   #1
RobbenStijn
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Location: Amsterdam

Join Date: Feb 2017
Posts: 12
Default Using MAC for analysis of proteins.

Dear all,

I'm completely new in the world of bioinformatics and I've got a fairly basic question for you. Any help would mean the world to me!

I found a dataset in which the ZNF778 was analyzed using MAC(2.10). The data holds information about MAC peaks, summits, FDR(%)-values and p-values. An example of the data is shown below:

# This file is generated by MACS version 1.4.1 20110627
# ARGUMENTS LIST:
# name = ./Processed/peaks/with_control/SI0335
# format = BAM
# ChIP-seq file = ./Processed/mapped/SI0335.sorted.nodup.bam
# control file = ./tmp/macs/SI0335.bkg.bam
# effective genome size = 2.70e+09
# band width = 300
# model fold = 10,30
# pvalue cutoff = 1.00e-03
# Large dataset will be scaled towards smaller dataset.
# Range for calculating regional lambda is: 1000 bps and 10000 bps

# tag size is determined as 50 bps
# total tags in treatment: 24340303
# total tags in control: 50009126
# d = 150
chr start end length summit tags -10*log10(pvalue) fold_enrichment FDR(%)
chr1 9911 10616 706 251 77 60.46 4.07 0.30
chr1 11119 11740 622 185 32 101.80 10.07 0.13
chr1 52255 53186 932 236 26 35.90 5.46 0.48
chr1 713754 714454 701 276 21 32.14 5.20 0.65
chr1 762008 763537 1530 295 52 75.37 6.63 0.29
chr1 823169 824143 975 740 37 76.59 5.89 0.28
chr1 839913 840369 457 311 19 73.91 10.48 0.28
chr1 851832 853636 1805 1399 85 168.64 10.71 0.07
chr1 855073 855672 600 269 18 30.24 5.32 0.77
chr1 856175 857276 1102 400 54 101.63 9.63 0.13

Now I'm interested in making a similar file, but for another protein (ZNF675). Especially the RDF(%)-values and the p-values are of interest for me.

Apparently I should use: https://github.com/taoliu/MACS/ but I have no idea how. Could anyone help me make a start?

Many thanks,

Stijn
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bam, bioinformatics, github, mac, sequencing

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