Noi/NOTES/2012-5-7: Difference between revisions
Jump to navigation
Jump to search
>Noi (Created page with "= Mapping of PGP1-F PGP1-iPS and H1 samples captured with LC Sciences probe set = * Refer to the capture experiment on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTE...") |
>Noi No edit summary |
||
Line 19: | Line 19: | ||
* Refer to the previous batch (111012_HL105), the sequences were trimmed 20bp from 5' end and also 6bp from 3' end since the quality of that run was not good as usual. However the quality of this run seemed to be good. I will trim only 20bp from the 5'end. | * Refer to the previous batch (111012_HL105), the sequences were trimmed 20bp from 5' end and also 6bp from 3' end since the quality of that run was not good as usual. However the quality of this run seemed to be good. I will trim only 20bp from the 5'end. | ||
== Trimming 20 bp from 5'end == | |||
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx7.txt | /home/kunzhang/bin/trimFastq.pl 20 80 > ./PGP1F-54C | |||
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx45.txt | /home/kunzhang/bin/trimFastq.pl 20 80 > ./PGP1iPS-54C | |||
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx76.txt | /home/kunzhang/bin/trimFastq.pl 20 80 > ./H1-54C | |||
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx77.txt | /home/kunzhang/bin/trimFastq.pl 20 80 > ./RC-1 |
Revision as of 00:05, 8 May 2012
Mapping of PGP1-F PGP1-iPS and H1 samples captured with LC Sciences probe set
- Refer to the capture experiment on: http://genome-tech.ucsd.edu/LabNotes/index.php/Noi/NOTES/2012-4-23
- The libraries were sequenced on 120426_HL118 run,lane 5.
- Sequencing data on genome-miner: /home/kunzhang/seqStore/120426_HL118/PE
Sample index
Sample IDs | Index |
PGP1-F 54C | CA-2-FA.Ind7.Sol |
PGP1-iPS 54C | CA-2-FA.Ind45.Sol |
H1 54C | CA-2-FA.Ind76.Sol |
RC-1 | CA-2-FA.Indx77.Sol |
- Note: RC-1 is the library from Baylor
- Refer to the previous batch (111012_HL105), the sequences were trimmed 20bp from 5' end and also 6bp from 3' end since the quality of that run was not good as usual. However the quality of this run seemed to be good. I will trim only 20bp from the 5'end.
Trimming 20 bp from 5'end
less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx7.txt | /home/kunzhang/bin/trimFastq.pl 20 80 > ./PGP1F-54C less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx45.txt | /home/kunzhang/bin/trimFastq.pl 20 80 > ./PGP1iPS-54C less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx76.txt | /home/kunzhang/bin/trimFastq.pl 20 80 > ./H1-54C less /home/kunzhang/seqStore/120426_HL118/PE/s_5_*_Indx77.txt | /home/kunzhang/bin/trimFastq.pl 20 80 > ./RC-1