Noi/NOTES/2012-5-7: Difference between revisions

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(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...")
 
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* 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

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