SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
miRNA mapping w/ Novoalign quiteconfused Bioinformatics 1 05-22-2012 08:23 AM
miRNA mapping w/ Novoalign quiteconfused RNA Sequencing 0 05-21-2012 07:09 PM
Can novoalign use FASTA as a reference format? (Specifically for mapping paired-end) oiiio Bioinformatics 2 04-18-2011 10:47 AM
Help:how to extrcate information from the output file of Novoalign mapping tools qc.share Illumina/Solexa 2 09-20-2010 07:31 PM
novoalign xh4a Bioinformatics 6 06-15-2010 10:10 AM

Reply
 
Thread Tools
Old 05-15-2013, 11:31 AM   #1
abh
Member
 
Location: philadelphia

Join Date: Aug 2012
Posts: 13
Default novoalign mapping

Hi,
I want to use novoalign to map reads - allowing up to 15 mismatches for 100 bp paired-end reads

I am new to novoalign(went through the manual) and confused with some of the options like -t,-x,-r etc..

so for 15 mismatches i should give something like

-t 500

what would be -x then?

this is the command line i am thinking to run

novoalign -d genome -f A_1.fq A_2.fq -t 500 -r All -o SAM > out.sam

Is this correct?


thank you
abh is offline   Reply With Quote
Reply

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 06:45 AM.


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