Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
De novo assembly using Trinity ankitarathore RNA Sequencing 5 10-28-2014 09:03 AM
de novo transcriptome Trinity Assembly concatenamers Dampor Bioinformatics 2 01-14-2014 02:34 AM
de novo assembly using Trinity versus Velvet-Oases Nol De novo discovery 8 10-26-2013 12:56 PM
get wrong when I do de novo assembly by trinity for two 22.6G reads file taoxiang180 Bioinformatics 4 08-20-2012 10:52 PM
Trinity - de novo transcriptome assembler samanta De novo discovery 2 07-29-2011 01:19 PM

Thread Tools
Old 10-12-2014, 07:31 AM   #1
Location: USA

Join Date: Aug 2014
Posts: 33
Default Trinity - de novo: how to start

I want to run Trinity to check what assembly I get de novo. I know I have to get something from my reads (I previously used other programs). Which command should I use to see if I get something? I've tryed but do not get anything. I have single reads in fq.
Pol8 is offline   Reply With Quote
Old 10-12-2014, 03:32 PM   #2
Junior Member
Location: MA

Join Date: Feb 2012
Posts: 1

first install trinity.

run, you will see the instructions how to use it. generally the command lines goes like: --seqType xx --JM xx reads.fq --CPU x --output xx

if paired ends, you need to specify right end and left end, such as --right xx.fq --left xx.fq
ilovefungi 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 03:10 AM.

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