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= HL111 (NP-BSPP-Hapmap-Nov15) mapping = * Note: ** In sequencing sample spreadsheet, these libraries were recored in lane 1-3, but they were actually loaded in lane 5-7. ** Libraries from two families (1362 and 1454) from HAPMAP plate, the 9 replicates for probe normalization and PGP1iPS treated with different bisulfite conversion kits (Zymoresearch and Imprint from Sigma). Also, one of UCLA sample (Indx94) was included in these libraries. * '''NP-BSPP-Hapmap-Nov15''' library normalization: [[http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2011-11-15]] {| {{table}} border = 1 | align="center" style="background:#f0f0f0;"|'''Indx''' | align="center" style="background:#f0f0f0;"|'''Sample ID''' |- | Indx10||GM11995 (wellID G7) |- | Indx11||GM11993 (wellID F2) |- | Indx12||**GM10861 (wellID A9) |- | Indx13||GM11992 (wellID C2 ) |- | Indx14||GM11994 (wellID G9 ) |- | Indx15||GM10860 (wellID F10) |- | Indx16||GM12813 (wellID E8) |- | Indx17||GM12802 (wellID E7) |- | Indx18||GM12815 (wellID G12) |- | Indx19||GM12812 (wellID F11) |- | Indx20||GM12814 (wellID A7) |- | Indx21||GM12801 (wellID D9) |- | Indx22||NA12156 (wellID B3)-1 |- | Indx23||NA12156 (wellID B3)-2 |- | Indx24||NA12156 (wellID B3)-3 |- | Indx25||NA12156 (wellID B3)-4 |- | Indx26||NA12156 (wellID B3)-5 |- | Indx27||NA12156 (wellID B3)-6 |- | Indx28||NA12156 (wellID B3)-7 |- | Indx29||NA12156 (wellID B3)-8 |- | Indx30||NA12156 (wellID B3)-9 |- | Indx41||**PGP1iPS |- | Indx42||PGP1iPS-IMPRINT |- | Indx94||UCLA-RO_Indx94 |} * Sequencing data is in genome-miner: '''/home/kunzhang/FreshReads/111209_SN1001''' == Merge and trim 27bp from 5' end == * Note: the last four digits in sample ID represent the family number less s_5_1_Indx10.txt s_5_2_Indx10.txt s_6_1_Indx10.txt s_6_2_Indx10.txt s_7_1_Indx10.txt s_7_2_Indx10.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM11995-1362<br> less s_5_1_Indx11.txt s_5_2_Indx11.txt s_6_1_Indx11.txt s_6_2_Indx11.txt s_7_1_Indx11.txt s_7_2_Indx11.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM11993-1362<br> less s_5_1_Indx12.txt s_5_2_Indx12.txt s_6_1_Indx12.txt s_6_2_Indx12.txt s_7_1_Indx12.txt s_7_2_Indx12.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM10861-1362<br> less s_5_1_Indx13.txt s_5_2_Indx13.txt s_6_1_Indx13.txt s_6_2_Indx13.txt s_7_1_Indx13.txt s_7_2_Indx13.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM11992-1362<br> less s_5_1_Indx14.txt s_5_2_Indx14.txt s_6_1_Indx14.txt s_6_2_Indx14.txt s_7_1_Indx14.txt s_7_2_Indx14.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM11994-1362<br> less s_5_1_Indx15.txt s_5_2_Indx15.txt s_6_1_Indx15.txt s_6_2_Indx15.txt s_7_1_Indx15.txt s_7_2_Indx15.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM10860-1362<br> less s_5_1_Indx16.txt s_5_2_Indx16.txt s_6_1_Indx16.txt s_6_2_Indx16.txt s_7_1_Indx16.txt s_7_2_Indx16.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM12813-1454<br> less s_5_1_Indx17.txt s_5_2_Indx17.txt s_6_1_Indx17.txt s_6_2_Indx17.txt s_7_1_Indx17.txt s_7_2_Indx17.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM12802-1454<br> less s_5_1_Indx18.txt s_5_2_Indx18.txt s_6_1_Indx18.txt s_6_2_Indx18.txt s_7_1_Indx18.txt s_7_2_Indx18.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM12815-1454<br> less s_5_1_Indx19.txt s_5_2_Indx19.txt s_6_1_Indx19.txt s_6_2_Indx19.txt s_7_1_Indx19.txt s_7_2_Indx19.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM12812-1454<br> less s_5_1_Indx20.txt s_5_2_Indx20.txt s_6_1_Indx20.txt s_6_2_Indx20.txt s_7_1_Indx20.txt s_7_2_Indx20.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM12814-1454<br> less s_5_1_Indx21.txt s_5_2_Indx21.txt s_6_1_Indx21.txt s_6_2_Indx21.txt s_7_1_Indx21.txt s_7_2_Indx21.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GM12801-1454<br> less s_5_1_Indx22.txt s_5_2_Indx22.txt s_6_1_Indx22.txt s_6_2_Indx22.txt s_7_1_Indx22.txt s_7_2_Indx22.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/NA12156-1408_1<br> less s_5_1_Indx23.txt s_5_2_Indx23.txt s_6_1_Indx23.txt s_6_2_Indx23.txt s_7_1_Indx23.txt s_7_2_Indx23.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/NA12156-1408_2<br> less s_5_1_Indx24.txt s_5_2_Indx24.txt s_6_1_Indx24.txt s_6_2_Indx24.txt s_7_1_Indx24.txt s_7_2_Indx24.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/NA12156-1408_3<br> less s_5_1_Indx25.txt s_5_2_Indx25.txt s_6_1_Indx25.txt s_6_2_Indx25.txt s_7_1_Indx25.txt s_7_2_Indx25.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/NA12156-1408_4<br> less s_5_1_Indx26.txt s_5_2_Indx26.txt s_6_1_Indx26.txt s_6_2_Indx26.txt s_7_1_Indx26.txt s_7_2_Indx26.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/NA12156-1408_5<br> less s_5_1_Indx27.txt s_5_2_Indx27.txt s_6_1_Indx27.txt s_6_2_Indx27.txt s_7_1_Indx27.txt s_7_2_Indx27.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/NA12156-1408_6<br> less s_5_1_Indx28.txt s_5_2_Indx28.txt s_6_1_Indx28.txt s_6_2_Indx28.txt s_7_1_Indx28.txt s_7_2_Indx28.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/NA12156-1408_7<br> less s_5_1_Indx29.txt s_5_2_Indx29.txt s_6_1_Indx29.txt s_6_2_Indx29.txt s_7_1_Indx29.txt s_7_2_Indx29.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/NA12156-1408_8<br> less s_5_1_Indx30.txt s_5_2_Indx30.txt s_6_1_Indx30.txt s_6_2_Indx30.txt s_7_1_Indx30.txt s_7_2_Indx30.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/NA12156-1408_9<br> less s_5_1_Indx41.txt s_5_2_Indx41.txt s_6_1_Indx41.txt s_6_2_Indx41.txt s_7_1_Indx41.txt s_7_2_Indx41.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/PGP1iPS-ZYMO<br> less s_5_1_Indx42.txt s_5_2_Indx42.txt s_6_1_Indx42.txt s_6_2_Indx42.txt s_7_1_Indx42.txt s_7_2_Indx42.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/PGP1iPS-IMPRINT<br> less s_5_1_Indx94.txt s_5_2_Indx94.txt s_6_1_Indx94.txt s_6_2_Indx94.txt s_7_1_Indx94.txt s_7_2_Indx94.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >/home/nplongth/Noi_scratch/HL111_BSPP-Hapmap_20111224/GK0281-004<br> == 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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