[Nelsonlab-analysis] Experiment list for U87

[Jordan M. <jme...@uc...>]

Below is a list of experiment aggregates I am running through my pipeline
for U87. Can people please review and tell me if there is anything else I am
missing?

Thanks,
Jordan

----

A) UCLA 50+50 LMP. (variant calling done)

*
/home/solexa/abi_datasets/Reports/U87_whole_genome_bfast_alignment/nhomer_bfast_alignment_reports-2010-1-15/bam/bfast.U87.old.flagdup.bam

B) 1024 Balanced Probes 50+50 LMP (2 slides) (variant calling done)

*
/home/solexa/abi_datasets/Reports/U87_whole_genome_bfast_alignment/nhomer_bfast_alignment_reports-2010-1-15/bam/bfast.solid0053_20091211_U87_LMP.flagdup.bam

C) 1024 Balanced Probes 50+35 (with degenerate 35bp) (2 slides) (variant
calling done)

*
/home/solexa/abi_datasets/Reports/U87_whole_genome_bfast_alignment/nhomer_bfast_alignment_reports-2010-1-15/bam/bfast.SELMA_20091214_1_U87_1024FAP_B1_F3.bam
*
/home/solexa/abi_datasets/Reports/U87_whole_genome_bfast_alignment/nhomer_bfast_alignment_reports-2010-1-15/bam/bfast.SELMA_20091214_1_U87_1024FAP_B1_R3.bam
*
/home/solexa/abi_datasets/Reports/U87_whole_genome_bfast_alignment/nhomer_bfast_alignment_reports-2010-1-15/bam/bfast.SELMA_20091214_2_U87_1024FAP_B2_F3.bam
*
/home/solexa/abi_datasets/Reports/U87_whole_genome_bfast_alignment/nhomer_bfast_alignment_reports-2010-1-15/bam/bfast.SELMA_20091214_2_U87_1024FAP_B2_R3.bam

D) Same as C but 50+25 instead of 50+35. (Still waiting on alignments from
Nils).


E) take B) and C) (forward only) and merge those together for pileups.
(Currently running).
What we want for this one is all the 1024 50mer reads merged together.

*
/home/solexa/abi_datasets/Reports/U87_whole_genome_bfast_alignment/nhomer_bfast_alignment_reports-2010-1-15/bam/bfast.solid0053_20091211_U87_LMP.flagdup.bam
*
/home/solexa/abi_datasets/Reports/U87_whole_genome_bfast_alignment/nhomer_bfast_alignment_reports-2010-1-15/bam/bfast.SELMA_20091214_1_U87_1024FAP_B1_F3.bam
*
/home/solexa/abi_datasets/Reports/U87_whole_genome_bfast_alignment/nhomer_bfast_alignment_reports-2010-1-15/bam/bfast.SELMA_20091214_2_U87_1024FAP_B2_F3.bam