SEQanswers

Go Back   SEQanswers > Applications Forums > Epigenetics



Similar Threads
Thread Thread Starter Forum Replies Last Post
MuTect short read preprocessing jing meng Bioinformatics 0 03-02-2016 10:14 PM
If I delete one sample do I have to redo DNA methylation data preprocessing HeidiLee Bioinformatics 1 05-08-2014 09:28 AM
% identity cutoff Chuckytah Metagenomics 0 04-30-2011 05:18 PM
amplicon preprocessing vs.shotgun processing litali 454 Pyrosequencing 4 02-16-2011 11:44 AM

Reply
 
Thread Tools
Old 03-27-2017, 08:34 AM   #1
jsaray
Junior Member
 
Location: IN my house

Join Date: Mar 2017
Posts: 1
Default Firebrowse Methylation Preprocessing CutOff

Hi All,

At the end of this website :

https://confluence.broadinstitute.or...n+Preprocessor

At the Clustering section is stated that "The default cutoff is .2, but it can be tuned based on the desired output file size".

I would want to tune this cutoff programatically, but I don't find how this can be achieved. I am using Python and I have :

rnaSEQ = firebrowse.Archives().StandardData(cohort='COADREAD',data_type='Methylation_Preprocess')

I reviewed all the parameters of StandardData action, but I don't find this cutoff parameter.

Best regards,
jsaray is offline   Reply With Quote
Reply

Tags
fire browse, methylation, pipeline, preprocessing

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:50 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO