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==Yi Zhang UNC-5caC/5fC == 8,506,009 reads for 5fC 39,354,845 reads for 5caC 12,518,460 reads for IgG 25,206,212 reads for Input ===Mapped with bowtie: (# alignments) === bowtie -n 2 --best --strata -l 28 -k 1 -m 1 -p 16 --phred64-quals --un $f.unmappable.txt /media/1TB_store1/Rui_Scratch/iGenome/Mus_musculus/UCSC/mm9/Sequence/BowtieIndex/genome $f $f.bowtie.map 2> $f.log > YZ_UNC-5caC-DIP.fastq.log <== # reads with at least one reported alignment: 20985742 (53.32%) # reads that failed to align: 2218974 (5.64%) # reads with alignments suppressed due to -m: 16150129 (41.04%) Reported 20985742 alignments to 1 output stream(s) > YZ_UNC-5fC-DIP.fastq.log <== # reads with at least one reported alignment: 3740642 (43.98%) # reads that failed to align: 970771 (11.41%) # reads with alignments suppressed due to -m: 3794596 (44.61%) Reported 3740642 alignments to 1 output stream(s) > YZ_UNC-IgG-DIP.fastq.log <== # reads with at least one reported alignment: 8023681 (64.09%) # reads that failed to align: 1072660 (8.57%) # reads with alignments suppressed due to -m: 3422119 (27.34%) Reported 8023681 alignments to 1 output stream(s) > YZ_UNC-Input.fastq.log <== # reads with at least one reported alignment: 16508323 (65.49%) # reads that failed to align: 3733811 (14.81%) # reads with alignments suppressed due to -m: 4964078 (19.69%) Reported 16508323 alignments to 1 output stream(s) ===Balance hits=== 2191 head -3740642 YZ_UNC-5caC-DIP.fastq.bowtie.map > sampled_YZ_UNC-5caC-DIP.fastq.bowtie.map & 2192 head -3740642 YZ_UNC-IgG-DIP.fastq.bowtie.map > sampled_YZ_UNC-IgG-DIP.fastq.bowtie.map & 2193 head -3740642 YZ_UNC-Input.fastq.bowtie.map > sampled_YZ_UNC-Input-DIP.fastq.bowtie.map & ===Peak calling using MACS=== macs14 -t sampled_YZ_UNC-5caC-DIP.fastq.bowtie.map -c sampled_YZ_UNC-IgG-DIP.fastq.bowtie.map -f BOWTIE -g mm -n 5caC-vsIgG -w --call-subpeaks > macs14_5caCvsIgG_balanced & macs14 -t sampled_YZ_UNC-5caC-DIP.fastq.bowtie.map -c sampled_YZ_UNC-Input-DIP.fastq.bowtie.map -f BOWTIE -g mm -n 5caC-vsInput -w --call-subpeaks > macs14_5caCvsInput_balanced & macs14 -t YZ_UNC-5fC-DIP.fastq.bowtie.map -c sampled_YZ_UNC-IgG-DIP.fastq.bowtie.map -f BOWTIE -g mm -n 5fC-vsIgG -w --call-subpeaks > macs14_5fCvsIgG_balanced & macs14 -t YZ_UNC-5fC-DIP.fastq.bowtie.map -c sampled_YZ_UNC-Input-DIP.fastq.bowtie.map -f BOWTIE -g mm -n 5fC-vsInput -w --call-subpeaks > macs14_5fCvsInput_balanced &
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