Re: [Useq-users] ORSS missing columns

[David N. <Dav...@hc...>]

Good catch Andrew,  yes genes not meeting the minimum # reads, and thus
not scored, had an inappropriate number of blanks inserted into the output.

I fixed this and posted it to SourceForge as USeq_8.3.4.

-cheers, D

On 7/6/12 10:53 AM, "Oler, Andrew (NIH/NIAID) [C]" <and...@ni...>
wrote:

>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)
>OCICB/OSMO/OD/NIAID/NIH
>
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