SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Taking care of multihits in RNA seq runs DavidMatthewsBristol RNA Sequencing 2 10-16-2012 09:06 PM
tophat max number of junctions per read? rcorbett Bioinformatics 0 11-23-2011 10:06 AM
Tophat 1.3.0 max-deletion-length option BUGFIX andrewmagis Bioinformatics 3 06-17-2011 11:07 PM
Tophat ignoring '--max-multihits' flag? polarise Bioinformatics 3 03-04-2011 11:28 AM
A question about tophat -g/--max-multihits option keycard Bioinformatics 2 12-29-2010 04:36 AM

Reply
 
Thread Tools
Old 06-07-2010, 02:26 PM   #1
brentp
Member
 
Location: salt lake city, UT

Join Date: Apr 2010
Posts: 72
Default tophat max-multihits not heeded

hi,
the docs for tophat specify that -g and --max-multihits should set the same value: "max_hits". it appears that only the -g option is used. i see the verbose arg it's expecting is "--max-gene-family" which is not documented.

btw python's optparse module [ http://docs.python.org/library/optparse.html ] is in the stdlib and is simpler than the getopt bindings.
brentp is offline   Reply With Quote
Old 06-14-2010, 09:54 AM   #2
brentp
Member
 
Location: salt lake city, UT

Join Date: Apr 2010
Posts: 72
Default

bumping.
i'm fairly certain this is a real bug!
is there a public development repo of tophat?
brentp is offline   Reply With Quote
Reply

Tags
rna-seq, tophat

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 12:39 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO