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== Combine data from different batches == less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0005-003a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0005-003a >./GK0005-003a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0005-004.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0005-004 >./GK0005-004<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0027-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0027-002 >./GK0027-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0050-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0050-002 >./GK0050-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0050-003.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0050-003 >./GK0050-003<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0050-004.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0050-004 >./GK0050-004<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0050-005a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0050-005a >./GK0050-005a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0091-001a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0091-001a >./GK0091-001a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0091-003.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0091-003 >./GK0091-003<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0100-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0100-002 >./GK0100-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0100-003.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0100-003 >./GK0100-003<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0122-001a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0122-001a >./GK0122-001a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0122-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0122-002 >./GK0122-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0122-003.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0122-003 >./GK0122-003<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0122-004.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0122-004 >./GK0122-004<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0123-001a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0123-001a >./GK0123-001a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0123-003.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0123-003 >./GK0123-003<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0123-004.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0123-004 >./GK0123-004<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0167-001a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0167-001a >./GK0167-001a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0167-003.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0167-003 >./GK0167-003<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0167-006.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0167-006 >./GK0167-006<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0178-001a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0178-001a >./GK0178-001a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0210-001.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0210-001 >./GK0210-001<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0210-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0210-002 >./GK0210-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0210-003a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0210-003a >./GK0210-003a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0241-001.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0241-001 >./GK0241-001<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0241-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0241-002 >./GK0241-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0241-003a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0241-003a >./GK0241-003a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0241-005.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0241-005 >./GK0241-005<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0271-001a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0271-001a >./GK0271-001a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0271-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0271-002 >./GK0271-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0271-004.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0271-004 >./GK0271-004<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0271-005.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0271-005 >./GK0271-005<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0277-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0277-002 >./GK0277-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0277-005.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0277-005 >./GK0277-005<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0281-001.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0281-001 >./GK0281-001<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0281-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0281-002 >./GK0281-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0281-003a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0281-003a >./GK0281-003a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0290-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0290-002 >./GK0290-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0290-003.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0290-003 >./GK0290-003<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0290-004a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0290-004a >./GK0290-004a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0295-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0295-002 >./GK0295-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0295-003a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0295-003a >./GK0295-003a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0295-004.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0295-004 >./GK0295-004<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0344-001a.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0344-001a >./GK0344-001a<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0344-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0344-002 >./GK0344-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0344-003.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0344-003 >./GK0344-003<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0359-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0359-002 >./GK0359-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0359-003.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0359-003 >./GK0359-003<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0359-006.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0359-006 >./GK0359-006<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0391-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0391-002 >./GK0391-002<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0396-004.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0396-004 >./GK0396-004 * Note: There were some problem in combining samples GK0281-001 and GK0281-002, so I needed to repeat them again using the same command. less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0281-001.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0281-001 >./GK0281-001<br> less /home/nplongth/Noi_scratch/combined_BSPP_UCLA-3batches_20111121/GK0281-002.gz /home/nplongth/Noi_scratch/HL111_RO_BSPP_UCLA_20120103/HL111_GK0281-002 >./GK0281-002<br> * Summary of sequencing and mapping statistic: [[Media:Updated_UCLA-RO-BSPP-mapping-hg19-summary_2012_01_04.xlsx]] * Whwn perform mapping on Troton cluster, there were few files which have very large size, so I needed to map them separately between the data from combined 3 batches and HL111 data. Then methylaFreq files were concatenated and generated BED file later. cat GK0091-003.fwd.pileup.methylFreq-3 HL111_GK0091-003.fwd.pileup.methylFreq > GK0091-003.fwd.pileup.methylFreq<br> cat GK0277-002.fwd.pileup.methylFreq-3 HL111_GK0277-002.fwd.pileup.methylFreq > GK0277-002.fwd.pileup.methylFreq<br> cat GK0277-005.fwd.pileup.methylFreq-3 HL111_GK0277-005.fwd.pileup.methylFreq > GK0277-005.fwd.pileup.methylFreq<br> perl /home/kunzhang/bin/methylFreq2BED.pl GK0091-003 10 <GK0091-003.fwd.pileup.methylFreq > GK0091-003.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl GK0277-002 10 <GK0277-002.fwd.pileup.methylFreq > GK0277-002.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl GK0277-005 10 <GK0277-005.fwd.pileup.methylFreq > GK0277-005.fwd.pileup.methylFreq.hg19.BED.txt<br> * Note: the GK0295-003a.fwd.pileup.methylFreq.hg19.BED.txt was missing from the list so I generated the BED file from methylmatrix file perl /home/kunzhang/bin/methylFreq2BED.pl GK0295-003a 10 <GK0295-003a.fwd.pileup.methylFreq > GK0295-003a.fwd.pileup.methylFreq.hg19.BED.txt * I have already generated mapping data from data from 3 batches, and all mapping data exit in the same folder (SNP, methylFreq and BED). I have copied only the data of sample >22M in the first batch and combined to the the data from 4 batches. * All mapping data are in genome-miner: /home/nplongth/Noi_scratch/combined_BSPP_UCLA-4batches_20120103/BSPP_UCLA.hg19.mapping-batch4
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