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| # Comment: | |
| # real name of file is 44_Mm04_WEAd_C11_chipseq_F.CHPv2.20141024.amd | |
| [Description] | |
| run_by_user pebert | |
| run_machine deep11 | |
| process CHPv2 | |
| date 20141024 | |
| run_start 2014-10-24 17:52:39.814533 | |
| dac_run_id DAC141024s277 | |
| software 0.2r375 | |
| run_end 2014-10-25 12:33:21.202072 | |
| [Inputs] | |
| GALvX_index 44_Mm04_WEAd_C11_H3K36me3_F.bwa.20141009.bam.bai,44_Mm04_WEAd_C11_H3K4me1_F.bwa.20141009.bam.bai,44_Mm04_WEAd_C11_Input_F.bwa.20141010.bam.bai,44_Mm04_WEAd_C11_H3K4me3_F.bwa.20141009.bam.bai,44_Mm04_WEAd_C11_H3K9me3_F.bwa.20141010.bam.bai,44_Mm04_WEAd_C11_H3K27ac_F.bwa.20141009.bam.bai,44_Mm04_WEAd_C11_H3K27me3_F.bwa.20141010.bam.bai | |
| GALvX_histone 44_Mm04_WEAd_C11_H3K36me3_F.bwa.20141009.bam,44_Mm04_WEAd_C11_H3K4me1_F.bwa.20141009.bam,44_Mm04_WEAd_C11_H3K4me3_F.bwa.20141009.bam,44_Mm04_WEAd_C11_H3K9me3_F.bwa.20141010.bam,44_Mm04_WEAd_C11_H3K27ac_F.bwa.20141009.bam,44_Mm04_WEAd_C11_H3K27me3_F.bwa.20141010.bam | |
| GALvX_input 44_Mm04_WEAd_C11_Input_F.bwa.20141010.bam | |
| [Outputs] | |
| samplesID.PROCESS.DATE.corplot.cormethod 44_Mm04_WEAd_C11_chipseq_F.CHPv2.20141024.corplot.pearson.png | |
| samplesID.PROCESS.DATE.fgprplot 44_Mm04_WEAd_C11_chipseq_F.CHPv2.20141024.fgpplot.png | |
| sampleID.PROCESS.DATE.gcbplot 44_Mm04_WEAd_C11_H3K36me3_F.CHPv2.20141024.gcbplot.png,44_Mm04_WEAd_C11_H3K4me1_F.CHPv2.20141024.gcbplot.png,44_Mm04_WEAd_C11_Input_F.CHPv2.20141024.gcbplot.png,44_Mm04_WEAd_C11_H3K4me3_F.CHPv2.20141024.gcbplot.png,44_Mm04_WEAd_C11_H3K9me3_F.CHPv2.20141024.gcbplot.png,44_Mm04_WEAd_C11_H3K27ac_F.CHPv2.20141024.gcbplot.png,44_Mm04_WEAd_C11_H3K27me3_F.CHPv2.20141024.gcbplot.png | |
| sampleID.PROCESS.DATE.gcbfreq 44_Mm04_WEAd_C11_H3K36me3_F.CHPv2.20141024.gcbfreq.txt,44_Mm04_WEAd_C11_H3K4me1_F.CHPv2.20141024.gcbfreq.txt,44_Mm04_WEAd_C11_Input_F.CHPv2.20141024.gcbfreq.txt,44_Mm04_WEAd_C11_H3K4me3_F.CHPv2.20141024.gcbfreq.txt,44_Mm04_WEAd_C11_H3K9me3_F.CHPv2.20141024.gcbfreq.txt,44_Mm04_WEAd_C11_H3K27ac_F.CHPv2.20141024.gcbfreq.txt,44_Mm04_WEAd_C11_H3K27me3_F.CHPv2.20141024.gcbfreq.txt | |
| sampleID.PROCESS.DATE._peaks.xls 44_Mm04_WEAd_C11_H3K36me3_F.CHPv2.20141024._peaks.xls,44_Mm04_WEAd_C11_H3K4me1_F.CHPv2.20141024._peaks.xls,44_Mm04_WEAd_C11_H3K4me3_F.CHPv2.20141024._peaks.xls,44_Mm04_WEAd_C11_H3K9me3_F.CHPv2.20141024._peaks.xls,44_Mm04_WEAd_C11_H3K27ac_F.CHPv2.20141024._peaks.xls,44_Mm04_WEAd_C11_H3K27me3_F.CHPv2.20141024._peaks.xls | |
| sampleID.PROCESS.DATE._peaks.broadPeak 44_Mm04_WEAd_C11_H3K36me3_F.CHPv2.20141024._peaks.broadPeak,44_Mm04_WEAd_C11_H3K4me1_F.CHPv2.20141024._peaks.broadPeak,44_Mm04_WEAd_C11_H3K9me3_F.CHPv2.20141024._peaks.broadPeak,44_Mm04_WEAd_C11_H3K27me3_F.CHPv2.20141024._peaks.broadPeak | |
| sampleID.PROCESS.DATE._peaks.gappedPeak 44_Mm04_WEAd_C11_H3K36me3_F.CHPv2.20141024._peaks.gappedPeak,44_Mm04_WEAd_C11_H3K4me1_F.CHPv2.20141024._peaks.gappedPeak,44_Mm04_WEAd_C11_H3K9me3_F.CHPv2.20141024._peaks.gappedPeak,44_Mm04_WEAd_C11_H3K27me3_F.CHPv2.20141024._peaks.gappedPeak | |
| sampleID.PROCESS.DATE._summits.bed 44_Mm04_WEAd_C11_H3K4me3_F.CHPv2.20141024._summits.bed,44_Mm04_WEAd_C11_H3K27ac_F.CHPv2.20141024._summits.bed | |
| sampleID.PROCESS.DATE._peaks.narrowPeak 44_Mm04_WEAd_C11_H3K4me3_F.CHPv2.20141024._peaks.narrowPeak,44_Mm04_WEAd_C11_H3K27ac_F.CHPv2.20141024._peaks.narrowPeak | |
| sampleIDs.PROCESS.DATE.bamcomp.scalemethod 44_Mm04_WEAd_C11_H3K36me3-log2-Input_F.CHPv2.20141024.bamcomp.SES.bw,44_Mm04_WEAd_C11_H3K4me1-log2-Input_F.CHPv2.20141024.bamcomp.SES.bw,44_Mm04_WEAd_C11_H3K4me3-log2-Input_F.CHPv2.20141024.bamcomp.SES.bw,44_Mm04_WEAd_C11_H3K9me3-log2-Input_F.CHPv2.20141024.bamcomp.readCount.bw,44_Mm04_WEAd_C11_H3K27ac-log2-Input_F.CHPv2.20141024.bamcomp.SES.bw,44_Mm04_WEAd_C11_H3K27me3-log2-Input_F.CHPv2.20141024.bamcomp.readCount.bw | |
| sampleID.PROCESS.DATE.bamcov.seqdepthnorm 44_Mm04_WEAd_C11_H3K36me3_F.CHPv2.20141024.bamcov.seqDepthNorm.bw,44_Mm04_WEAd_C11_H3K4me1_F.CHPv2.20141024.bamcov.seqDepthNorm.bw,44_Mm04_WEAd_C11_Input_F.CHPv2.20141024.bamcov.seqDepthNorm.bw,44_Mm04_WEAd_C11_H3K4me3_F.CHPv2.20141024.bamcov.seqDepthNorm.bw,44_Mm04_WEAd_C11_H3K9me3_F.CHPv2.20141024.bamcov.seqDepthNorm.bw,44_Mm04_WEAd_C11_H3K27ac_F.CHPv2.20141024.bamcov.seqDepthNorm.bw,44_Mm04_WEAd_C11_H3K27me3_F.CHPv2.20141024.bamcov.seqDepthNorm.bw | |
| sampleID.PROCESS.DATE.ctrlreg 44_Mm04_WEAd_C11_H3K36me3_F.CHPv2.20141024.ctrlreg.png,44_Mm04_WEAd_C11_H3K4me1_F.CHPv2.20141024.ctrlreg.png,44_Mm04_WEAd_C11_H3K4me3_F.CHPv2.20141024.ctrlreg.png,44_Mm04_WEAd_C11_H3K9me3_F.CHPv2.20141024.ctrlreg.png,44_Mm04_WEAd_C11_H3K27ac_F.CHPv2.20141024.ctrlreg.png,44_Mm04_WEAd_C11_H3K27me3_F.CHPv2.20141024.ctrlreg.png | |
| [References] | |
| filtered_regions mm10_ENC.DKFZ_blacklist.bed | |
| reference_genome GRCm38mm10.2bit | |
| plot_regions histone_ChIP_pos_ctrl_regions_mm10.bed | |
| [Parameters] | |
| labels 44_Mm04_WEAd_C11_H3K36me3_F,44_Mm04_WEAd_C11_H3K4me1_F,44_Mm04_WEAd_C11_Input_F,44_Mm04_WEAd_C11_H3K4me3_F,44_Mm04_WEAd_C11_H3K9me3_F,44_Mm04_WEAd_C11_H3K27ac_F,44_Mm04_WEAd_C11_H3K27me3_F | |
| all_median_fraglen 190 | |
| numproc 16 | |
| genomesize 2650000000 | |
| h3k36me3_median_fraglen 239 | |
| h3k4me1_median_fraglen 190 | |
| input_median_fraglen 121 | |
| h3k4me3_median_fraglen 173 | |
| h3k9me3_median_fraglen 252 | |
| h3k27ac_median_fraglen 175 | |
| h3k27me3_median_fraglen 255 | |
| h3k36me3_broad True | |
| h3k36me3_name_prefix 44_Mm04_WEAd_C11_H3K36me3_F.CHPv2.20141024. | |
| h3k4me1_broad True | |
| h3k4me1_name_prefix 44_Mm04_WEAd_C11_H3K4me1_F.CHPv2.20141024. | |
| h3k4me3_broad False | |
| h3k4me3_name_prefix 44_Mm04_WEAd_C11_H3K4me3_F.CHPv2.20141024. | |
| h3k9me3_broad True | |
| h3k9me3_name_prefix 44_Mm04_WEAd_C11_H3K9me3_F.CHPv2.20141024. | |
| h3k27ac_name_prefix 44_Mm04_WEAd_C11_H3K27ac_F.CHPv2.20141024. | |
| h3k27ac_broad False | |
| h3k27me3_name_prefix 44_Mm04_WEAd_C11_H3K27me3_F.CHPv2.20141024. | |
| h3k27me3_broad True | |
| h3k36me3_scaling_method SES | |
| h3k4me1_scaling_method SES | |
| h3k4me3_scaling_method SES | |
| h3k9me3_scaling_method readCount | |
| h3k27ac_scaling_method SES | |
| h3k27me3_scaling_method readCount | |
| [Metrics] | |
| read_count_h3k36me3 149416256 | |
| peak_count_h3k36me3 41290 | |
| frip_h3k36me3 0.56 | |
| read_count_h3k4me1 123384550 | |
| peak_count_h3k4me1 103773 | |
| frip_h3k4me1 0.46 | |
| read_count_input 214965156 | |
| read_count_h3k4me3 117531972 | |
| peak_count_h3k4me3 30418 | |
| frip_h3k4me3 0.62 | |
| read_count_h3k9me3 232803908 | |
| peak_count_h3k9me3 125819 | |
| frip_h3k9me3 0.44 | |
| read_count_h3k27ac 98939872 | |
| peak_count_h3k27ac 98324 | |
| frip_h3k27ac 0.51 | |
| read_count_h3k27me3 280728496 | |
| peak_count_h3k27me3 98020 | |
| frip_h3k27me3 0.27 |