Public data, Mikkelsen et al.
Public data can be used in 2 ways:
- download processed data uploaded by the authors
- download raw data
Use the first one save time but rely on the authors's workflow
Fetch fastq
Go on NCBI GEO
Then select RunSelector.
From a Cell paper from 2010 and belong to this dataset:
Specifically we want to look at these samples:
te input control they used for normalization:
Download SRR_Acc_List.txt in /scratch/users/aginolhac/chip-seq/Mikkelsen
fastq-dump is a tool from NCBI, part of the sra-tools, available for free. Install this program.
then fetch and compress
parallel -j 6 --progress "fastq-dump --gzip {}" :::: SRR_Acc_List.txt
mapped with paleomix
file available here
paleomix bam_pipeline --bwa-max-threads=4 --max-threads=12 mikkelsen.yml
last for ~ 3 hours 30 minutes
peak calling
H3K4
macs2 callpeak -t Mikkelsen_3T3L1_t2_H3K4me3.GRCm38.p3.bam \
-c Mikkelsen_3T3L1_WCE.GRCm38.p3.bam \
-f BAM -g mm -n 3T3L1_t2_H3K4 -B -q 0.01 --outdir 3T3L1_t2_H3K4 &
macs2 callpeak -t Mikkelsen_3T3L1_t3_H3K4me3.GRCm38.p3.bam \
-c Mikkelsen_3T3L1_WCE.GRCm38.p3.bam \
-f BAM -g mm -n3T3L1_t3_H3K4 -B -q 0.01 --outdir 3T3L1_t3_H3K4
H3K27
macs2 callpeak -t Mikkelsen_3T3L1_t2_H3K27ac.GRCm38.p3.bam \
-c Mikkelsen_3T3L1_WCE.GRCm38.p3.bam --broad \
-f BAM -g mm -n 3T3L1_t2_H3K27ac -B -q 0.01 --outdir 3T3L1_t2_H3K27ac &
macs2 callpeak -t Mikkelsen_3T3L1_t3_H3K27ac.GRCm38.p3.bam \
-c Mikkelsen_3T3L1_WCE.GRCm38.p3.bam --broad \
-f BAM -g mm -n3T3L1_t3_H3K27ac -B -q 0.01 --outdir 3T3L1_t3_H3K27ac