Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: SICER error: SICER is not available for the genome
0
gravatar for gskbioinfo143
2.2 years ago by
gskbioinfo143 • 0
gskbioinfo143 • 0 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
enhancement sicer genome database • 705 views
ADD COMMENT • link •
modified 2.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.2 years ago by gskbioinfo143 • 0
0
gravatar for Jennifer Hillman Jackson
2.2 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.2 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.2 years ago by gskbioinfo143 • 0
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 175 users visited in the last hour