Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
mapping on to custom reference sequence PratikC Bioinformatics 14 02-06-2019 04:41 PM
mapping quality tophat2 - always 255 vbernard Bioinformatics 1 07-03-2012 01:51 AM
Low mapping percentage with TopHat2 DerSeb RNA Sequencing 3 06-05-2012 05:35 AM
Mapping to a custom reference LauraR Bioinformatics 1 01-26-2012 03:01 PM
The optimal options for TopHat in mapping 35bp SOLiD reads holywoool Bioinformatics 0 09-22-2011 07:10 PM

Thread Tools
Old 10-23-2013, 10:36 AM   #1
Junior Member
Location: Pittsburgh

Join Date: May 2013
Posts: 7
Default Tophat2 default and custom mapping options

Hi All,

I've been running this tophat2 command, tophat2 -i 20 -I 1200 -g 1 for mapping human RNAseq reads. These numbers are given to me by some others and I am not sure if these settings are appropriate for our application and also if we should stick with default values of Tophat2 rather than using these custom values.

I would very much appreciate if anybody can share values of custom settings of tophat2 for mapping human RNAseq reads.

Thanks in advance.

akh22 is offline   Reply With Quote

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 06:12 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO