Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Optimizing tophat running time kevin9y9 RNA Sequencing 1 03-13-2013 07:09 AM
Optimizing tophat mapping for mixed RNA-Seq data bob-loblaw Bioinformatics 5 02-15-2013 02:22 AM
PubMed: Optimizing Illumina Next-Generation Sequencing library preparation for extrem Newsbot! Literature Watch 0 01-05-2012 10:20 AM
Optimizing settings for mapping 100bp RNA-seq reads with tophat seqhorn Bioinformatics 3 10-21-2011 10:40 PM
Tophat options to report unaligned reads and controlling Bowtie options Siva Bioinformatics 0 10-15-2010 07:38 PM

Thread Tools
Old 09-16-2013, 10:41 AM   #1
Junior Member
Location: Delaware

Join Date: Apr 2013
Posts: 1
Question MIREAP - optimizing options for different species?

Hello all,

I'm trying to discover novel miRNAs in avian species and I was wondering if anyone has any experience with using MIREAP and customizing the options for non-mammalian genomes? The documentation for MIREAP is sparse but the output is great once you get it working.

There are four options that define the maximum and minimum miRNA sequence length and the maximum and minimum miRNA reference length. The min-max sequence lengths default to 18-26. The min-max reference sequence lengths default to 20-24. My concern is that the numbers don't match up and I'm not sure why. I understand mammalian miRNAs are ~22nt long, but in avian species miRNAs are ~23nt in length. As such, can I move all default parameters up 1nt or do I expand the parameters to include the low and high range (whether this is 20-26 or dependent on sequence length distribution within a sample set).

I just want to make sure I'm squeezing as much out of it without causing issues by tweaking the options too much.
tjcarr is offline   Reply With Quote

mireap, mirna identification, mirna-seq

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 08:55 PM.

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