Noi/NOTES/2012-1-2
- Labnote Link:[[1]]
HL111-BSPP_UCLA (batch4) mapping[edit]
- Note: the libraries were allocated in HL111 run lane4
- Sequencing data is in genome-miner:/home/kunzhang/FreshReads/111209_SN1001
- Update current raw sequences on genome-miner: /media/SeqStore2/111209_HL111/BSPP
Merge and trim 27bp from 5' end[edit]
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx4.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx4.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0091-003
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx5.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx5.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0359-003
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx6.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx6.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0005-003a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx7.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx7.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0050-004
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx10.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx10.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0050-003
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx11.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx11.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0241-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx12.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx12.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0091-001a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx13.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx13.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0359-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx14.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx14.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0123-003
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx15.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx15.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0295-004
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx16.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx16.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0295-003a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx18.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx18.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0271-001a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx20.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx20.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0167-001a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx21.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx21.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0391-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx22.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx22.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0210-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx24.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx24.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0271-004
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx26.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx26.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0210-001
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx28.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx28.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0295-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx30.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx30.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0123-001a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx31.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx31.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0167-006
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx36.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx36.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0271-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx37.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx37.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0050-005a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx39.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx39.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0122-003
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx40.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx40.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0290-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx42.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx42.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0241-005
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx44.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx44.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0241-003a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx45.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx45.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0277-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx46.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx46.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0100-003
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx47.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx47.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0050-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx48.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx48.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0122-004
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx49.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx49.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0210-003a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx50.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx50.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0281-003a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx52.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx52.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0122-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx53.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx53.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0281-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx55.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx55.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0359-006
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx60.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx60.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0005-004
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx62.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx62.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0167-003
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx63.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx63.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0122-001a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx66.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx66.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0344-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx67.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx67.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0100-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx68.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx68.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0027-002
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx69.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx69.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0281-001
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx71.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx71.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0396-004
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx72.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx72.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0344-001a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx74.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx74.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0290-003
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx76.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx76.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0241-001
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx77.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx77.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0277-005
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx83.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx83.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0290-004a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx85.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx85.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0271-005
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx92.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx92.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0178-001a
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx95.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx95.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0344-003
less /home/kunzhang/FreshReads/111209_SN1001/s_4_1_Indx96.txt /home/kunzhang/FreshReads/111209_SN1001/s_4_2_Indx96.txt | /home/kunzhang/bin/trimFastq.pl 27 83 >./HL111_GK0123-004
Combine data from different batches[edit]
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
- 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
cat GK0277-002.fwd.pileup.methylFreq-3 HL111_GK0277-002.fwd.pileup.methylFreq > GK0277-002.fwd.pileup.methylFreq
cat GK0277-005.fwd.pileup.methylFreq-3 HL111_GK0277-005.fwd.pileup.methylFreq > GK0277-005.fwd.pileup.methylFreq
perl /home/kunzhang/bin/methylFreq2BED.pl GK0091-003 10 <GK0091-003.fwd.pileup.methylFreq > GK0091-003.fwd.pileup.methylFreq.hg19.BED.txt
perl /home/kunzhang/bin/methylFreq2BED.pl GK0277-002 10 <GK0277-002.fwd.pileup.methylFreq > GK0277-002.fwd.pileup.methylFreq.hg19.BED.txt
perl /home/kunzhang/bin/methylFreq2BED.pl GK0277-005 10 <GK0277-005.fwd.pileup.methylFreq > GK0277-005.fwd.pileup.methylFreq.hg19.BED.txt
- 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