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berman-lab / ymap

YMAP - Yeast Mapping Analysis Pipeline : An online pipeline for the analysis of yeast genomic datasets.
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Wrong read of CNV #48

Closed ghost closed 7 years ago

ghost commented 7 years ago

It appears there are places were the CNV read should be zero and yet it is as the baseline value. For example in the following setting Genome: Candida glabrata CBS138 (ver. 02-m04-r01) DataSet: 195L_R_CCGTCC_L002_R1 hapmap: CBS_vs_BG2

in chromosome A in the middle there is a place with zero reads and it appears white yet the CNV at baseline. (image attached)

fig cnv-snp-map 1

darrenabbey commented 7 years ago

There is CNV data evident in that region, but there is no SNP ratio data. The amount of CNV data is minimal, however, which results in poor numerical value determinations from the Gaussian fitting method used.

I think there is also be an explicit check for actual zero data in local regions, which would then default to assumed baseline CNV values. This was put in place to bypass an annoying divide-by-zero error for tiny regions of zero-data that did not appear informative. I believe this is done in the find_car_sizes function.

Usually, when a region is deleted there are some minimal reads mapped to the region anyhow, which allows the visualization to show the appropriate values. This prevented the bypass from being obviously a problem until now.

On Sep 12, 2016 8:29 AM, "GuyKha" notifications@github.com wrote:

It appears there are places were the CNV read so be zero and yet it is as the baseline value. For example in the following setting Genome: Candida glabrata CBS138 (ver. 02-m04-r01) DataSet: 195L_R_CCGTCC_L002_R1 hapmap: CBS_vs_BG2

in chromosome A in the middle there is a place with zero reads and it appears white yet the CNV at baseline. (image attached)

https://camo.githubusercontent.com/901819f46ec56d954c2d7e32443074133a6cb55a/687474703a2f2f6c6f63616c686f73742f75736572732f74657374757365722f70726f6a656374732f696e76616c69642f6669672e434e562d534e502d6d61702e312e706e67 [image: fig cnv-snp-map 1] https://cloud.githubusercontent.com/assets/20476730/18437527/17156dc2-7906-11e6-855f-29638fd555f6.png

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