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== Mapping to hg19 on Triton cluster == * Note: ** Since some files are very big, they failed to get the output files. I need to split those files (on Triton cluster) and do mapping again. ** I used head and tail commands instead of split command. head -111017824 GM10861-1362 > GM10861-1362-1<br> head -106854184 GM11992-1362 > GM11992-1362-1<br> head -122652416 GM11995-1362 > GM11995-1362-1<br> head -108824480 GM12802-1454 > GM12802-1454-1<br> head -109761668 GM12812-1454 > GM12812-1454-1<br> head -114040252 GM12813-1454 > GM12813-1454-1<br> head -109525956 GM12814-1454 > GM12814-1454-1<br> head -124399152 GM12815-1454 > GM12815-1454-1<br> head -113341284 NA12156-1408_1 > NA12156-1408_1-1<br> head -104618848 NA12156-1408_3 > NA12156-1408_3-1<br> head -109221100 NA12156-1408_4 > NA12156-1408_4-1<br> head -114618216 NA12156-1408_5 > NA12156-1408_5-1<br> head -111514412 NA12156-1408_6 > NA12156-1408_6-1<br> tail -111017824 GM10861-1362 > GM10861-1362-2<br> tail -106854184 GM11992-1362 > GM11992-1362-2<br> tail -122652416 GM11995-1362 > GM11995-1362-2<br> tail -108824480 GM12802-1454 > GM12802-1454-2<br> tail -109761668 GM12812-1454 > GM12812-1454-2<br> tail -114040252 GM12813-1454 > GM12813-1454-2<br> tail -109525956 GM12814-1454 > GM12814-1454-2<br> tail -124399152 GM12815-1454 > GM12815-1454-2<br> tail -113341284 NA12156-1408_1 > NA12156-1408_1-2<br> tail -104618848 NA12156-1408_3 > NA12156-1408_3-2<br> tail -109221100 NA12156-1408_4 > NA12156-1408_4-2<br> tail -114618216 NA12156-1408_5 > NA12156-1408_5-2<br> tail -111514412 NA12156-1408_6 > NA12156-1408_6-2<br> * '''After mapping, the methylFreq files were concatenated (on genome-miner)''' cat GM10861-1362-1.fwd.pileup.methylFreq GM10861-1362-2.fwd.pileup.methylFreq > GM10861-1362.fwd.pileup.methylFreq<br> cat GM11992-1362-1.fwd.pileup.methylFreq GM11992-1362-2.fwd.pileup.methylFreq > GM11992-1362.fwd.pileup.methylFreq<br> cat GM11995-1362-1.fwd.pileup.methylFreq GM11995-1362-2.fwd.pileup.methylFreq > GM11995-1362.fwd.pileup.methylFreq<br> cat GM12802-1454-1.fwd.pileup.methylFreq GM12802-1454-2.fwd.pileup.methylFreq > GM12802-1454.fwd.pileup.methylFreq<br> cat GM12812-1454-1.fwd.pileup.methylFreq GM12812-1454-2.fwd.pileup.methylFreq > GM12812-1454.fwd.pileup.methylFreq<br> cat GM12813-1454-1.fwd.pileup.methylFreq GM12813-1454-2.fwd.pileup.methylFreq > GM12813-1454.fwd.pileup.methylFreq<br> cat GM12814-1454-1.fwd.pileup.methylFreq GM12814-1454-2.fwd.pileup.methylFreq > GM12814-1454.fwd.pileup.methylFreq<br> cat GM12815-1454-1.fwd.pileup.methylFreq GM12815-1454-2.fwd.pileup.methylFreq > GM12815-1454.fwd.pileup.methylFreq<br> cat NA12156-1408_1-1.fwd.pileup.methylFreq NA12156-1408_1-2.fwd.pileup.methylFreq > NA12156-1408_1.fwd.pileup.methylFreq<br> cat NA12156-1408_3-1.fwd.pileup.methylFreq NA12156-1408_3-2.fwd.pileup.methylFreq > NA12156-1408_3.fwd.pileup.methylFreq<br> cat NA12156-1408_4-1.fwd.pileup.methylFreq NA12156-1408_4-2.fwd.pileup.methylFreq > NA12156-1408_4.fwd.pileup.methylFreq<br> cat NA12156-1408_5-1.fwd.pileup.methylFreq NA12156-1408_5-2.fwd.pileup.methylFreq > NA12156-1408_5.fwd.pileup.methylFreq<br> cat NA12156-1408_6-1.fwd.pileup.methylFreq NA12156-1408_6-2.fwd.pileup.methylFreq > NA12156-1408_6.fwd.pileup.methylFreq<br> * '''Generated BED files by methylFreq2BED.pl script (on genome-miner).''' perl /home/kunzhang/bin/methylFreq2BED.pl GM10861-1362 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/GM10861-1362.fwd.pileup.methylFreq > GM10861-1362.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl GM11992-1362 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/GM11992-1362.fwd.pileup.methylFreq > GM11992-1362.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl GM11995-1362 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/GM11995-1362.fwd.pileup.methylFreq > GM11995-1362.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl GM12802-1454 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/GM12802-1454.fwd.pileup.methylFreq > GM12802-1454.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl GM12812-1454 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/GM12812-1454.fwd.pileup.methylFreq > GM12812-1454.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl GM12813-1454 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/GM12813-1454.fwd.pileup.methylFreq > GM12813-1454.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl GM12814-1454 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/GM12814-1454.fwd.pileup.methylFreq > GM12814-1454.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl GM12815-1454 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/GM12815-1454.fwd.pileup.methylFreq > GM12815-1454.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl NA12156-1408_1 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/NA12156-1408_1.fwd.pileup.methylFreq > NA12156-1408_1.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl NA12156-1408_3 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/NA12156-1408_3.fwd.pileup.methylFreq > NA12156-1408_3.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl NA12156-1408_4 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/NA12156-1408_4.fwd.pileup.methylFreq > NA12156-1408_4.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl NA12156-1408_5 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/NA12156-1408_5.fwd.pileup.methylFreq > NA12156-1408_5.fwd.pileup.methylFreq.hg19.BED.txt<br> perl /home/kunzhang/bin/methylFreq2BED.pl NA12156-1408_6 10 <HAPMAP_mapping.data_hg19/HAPMAP.methylFreq/NA12156-1408_6.fwd.pileup.methylFreq > NA12156-1408_6.fwd.pileup.methylFreq.hg19.BED.txt * To generate methylation matrix I used Dinh'script '''(allBED2Matrix_DD.pl)''' to run since I got the wrong number of samples after getting ~81,332 line in the matrix. Dinh's script uses list of file instead of directory location. * For exmple, ** '''GK0281-004''' '''HAPMAP.BED/GK0281-004.fwd.pileup.methylFreq.hg19.BED.txt''' --> the first column is the display name, and the second column is the input file ** To run --> '''./allBED2Matrix_DD.pl bed_list 40 1 0.'''1 (no need to put output file)
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