SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bed to BedGraph ayushraman Bioinformatics 4 08-20-2015 07:01 AM
To Assemble or not to Assemble (Illumina short reads-microbial metagenomic data) Andres_Gomez Bioinformatics 0 09-30-2013 01:52 PM
Uploading bedgraph files pthomp Bioinformatics 0 05-17-2012 12:13 PM
wiggle or bedGraph statsteam Bioinformatics 3 10-06-2009 11:49 AM

Reply
 
Thread Tools
Old 09-04-2014, 04:17 AM   #1
Feng Tian
Junior Member
 
Location: Beijing, China

Join Date: Sep 2014
Posts: 1
Question Using bedgraph to transcript assemble

Hello, I got some RNA-seq data in bedgraph format and I want to use it for transcript assembly but Cufflinks cannot accept bedgraph as input. So is there some ways to transform bedgraph into sam format
Feng Tian is offline   Reply With Quote
Old 09-04-2014, 11:05 PM   #2
WhatsOEver
Senior Member
 
Location: Germany

Join Date: Apr 2012
Posts: 215
Default

While there are possibilities to convert the data, this is not what you are looking for.
The bedgraph format just gives you coordinates of the reference. You don't have any read sequence information in it and transcript assembly doesn't make much sense then.
Wherever you got your data from, ask for the original files that were used to generate the bedgraph file which has to be either sam/bam or fastq.
WhatsOEver is offline   Reply With Quote
Reply

Tags
bedgraph, cufflinks-2.2.1, sam

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 03:59 PM.


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