Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Shall I post splice-junction tools problems in bioinformatics or RNA-seq forum? kanewong General 1 04-11-2013 04:01 AM
Suggestions on trimming RNA-seq file and compare splice-junction tools results kanewong Bioinformatics 0 04-10-2013 12:30 AM
An anxious Msc student doing a splice-junction tools research project kanewong Introductions 4 04-07-2013 07:04 AM
RNA-Seq: MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery. Newsbot! Literature Watch 2 10-14-2010 08:35 AM

Thread Tools
Old 04-11-2013, 06:59 AM   #1
Location: hk

Join Date: Apr 2013
Posts: 16
Default How to trim RNA-seq file and compare splice-junction tools results

Hi all,

I am a newbie to bioinformatics and this forum. Hopefully I am posting my question in a proper way.

I am currently running tophat, splicemap and mapsplice on a set of RNA-seq data, I would like to know the following matters:

1. Is there any easy-to-use tools to trim a RNA-seq file into a shorter read-length one? I made a search on the internet and found that perl seems to be one of the solution. Since I haven't learned perl before, I wonder if there are any other tools which are easier to use.

2. After running the splice-junction tools, I want to compare the overlap of their results. I made a search and a webiste suggests I can use Rsamtools and GenomicRanges
packages of R software to do so. Is it an easy and common way to compare splice-junction tools results?

As long as the tool is easy to use, it is fine for me.

Thank you very much
kanewong 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 10:35 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO