Noi/NOTES/2011-12-25
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: [[1]]
Indx | 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-digit of sample ID represents 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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq
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.fastq