Question: SICER error: SICER is not available for the genome
0
gravatar for gskbioinfo143
21 months ago by
gskbioinfo1430 wrote:

Hi im getting error while using SICER on data sets SRX681547 and SRX681548 it shows SICER is not available for the genome . i checked this web https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset and edited the genome Hg38 to all data but still the error shows the same.

please need help

Thanks

ADD COMMENTlink modified 21 months ago by Jennifer Hillman Jackson25k • written 21 months ago by gskbioinfo1430
0
gravatar for Jennifer Hillman Jackson
21 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The SICER tool as currently wrapped only supports the following builds (from the sicer_wrapper.py source code):

VALID_BUILDS = [ 'mm8', 'mm9', 'hg18', 'hg19', 'dm2', 'dm3', 'sacCer1', 'pombe', 'rn4', 'tair8' ]

I opened this ticket requesting that the tool be updated to include more builds, including hg38. https://github.com/galaxyproject/tools-devteam/issues/390. Meanwhile, if working with human data, hg19 is the most current build that can be used.

Thanks for your comments,

ADD COMMENTlink written 21 months ago by Jennifer Hillman Jackson25k

hi i tried to analyze two datasets SRX681547 and SRX681548 keeping one as treatment and other as control to find unique enriched regions or peaks using SICER tool but analysis fails(hg19 database). Need help please the analysis is at shashikanth20@gmail.com account

ADD REPLYlink written 21 months ago by gskbioinfo1430
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