Kun:LabNotes/CpgSeq/2009-6-9: Difference between revisions
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*To do this, the all CGs in the H2 arms were replaced by YGs. Then resulting sequences were concatenated with two flanking sequences. | *To do this, the all CGs in the H2 arms were replaced by YGs. Then resulting sequences were concatenated with two flanking sequences. | ||
ATCCGATC---H2---GTCGGACCTC | ATCCGATC---H2---GTCGGACCTC | ||
[[Media:IDT_Cpg97k_suppressor_oligos.xls|Oligo sequences submitted to IDT]] |
Revision as of 15:23, 9 June 2009
Data analysis of the end-sequencing results from the two Cpg97k captured libraries
- The pre-normalized and normalized libraries from NA21070 were prepared by Jie.
- The concentration was over estimated by ~10-fold, which led to only 1/10 of reads per lane than were expected.
Pre-normalization Post-normalization # raw reads 633,866 594,422 # mappable reads 516,594 429,326 # targets found 34,695 45,422
File:Cpg97k-endSeq-normalization-scatterplot.png File:Cpg97k-endSeq-normalization-ranked-curves.png
Suppressor oligos
- The probes were sorted based on the read counts in the post-normalized library.
- 96 suppressor oligos were design for the top 96 targets.
- To do this, the all CGs in the H2 arms were replaced by YGs. Then resulting sequences were concatenated with two flanking sequences.
ATCCGATC---H2---GTCGGACCTC Oligo sequences submitted to IDT