[Useq-users] ORSS missing columns

[Oler, A. (NIH/N. [C] <and...@ni...>]

Hi David,

I'm using OverdispersedRegionScanSeqs in USeq 8.2.3 and it looks like the tFPKM and cFPKM columns are missing for genes that have low counts in the all.xls file.  Because the columns are missing, it looks like the FPKM is actually pretty high in some cases (e.g., tFPKM is 3 in row 15383 in the attached image, but my guess is this should actually be the counts for #T1, not the FPKM).  This retains a lot of genes that should be excluded when I filter by FPKM columns.

My command line:



Thanks,

Andrew

Andrew Oler, Ph.D.
High-Throughput Sequencing Bioinformatics Specialist
Contractor - Medical Science & Computing, Inc.
Computational Biology Section
Bioinformatics and Computational Biosciences Branch (BCBB)
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