BED to ELAND/bowtie/MAQ ?

ewilbanks · 08-20-2009, 12:09 PM

Hi all,

I'm working with a .bed format file of illumina reads and I don't have the original alignment file. A program I'm working with can read in bowtie, eland, maq or modified bed (see below) but not regular bed files!

Anyone have a good recommendation for ways to convert .bed to one of these file formats?

Thanks!!!

Lizzy

dawe · 08-21-2009, 01:25 AM

I guess you cannot go back to alignment data, because bed files only retain mapping positions (plus possibly some other information). You may do a couple of things:
1- simulate alignment data assuming all your reads are perfect matches with fake quality (possibly playing with awk and fasta reading tools)
2- try to fit your bed into the modified bed.
Which "modified bed" format are we talking about? How do your data look like?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Bowtie output to BED format	polsum	Bioinformatics	11	02-20-2013 12:00 AM
Eland-to-Bed algorithm	joseph	Bioinformatics	27	11-19-2012 07:12 PM
Eland to Bed	__sequence	Illumina/Solexa	0	06-08-2011 05:07 AM
MAQ .map files to .bed/.sam for MACS	calexand	Bioinformatics	1	01-20-2011 09:14 AM
How to convert eland file to BED format	huo	Bioinformatics	1	01-19-2011 11:43 AM

08-20-2009, 12:09 PM	#1
ewilbanks Member Location: Davis, CA Join Date: Mar 2009 Posts: 82	BED to ELAND/bowtie/MAQ ? Hi all, I'm working with a .bed format file of illumina reads and I don't have the original alignment file. A program I'm working with can read in bowtie, eland, maq or modified bed (see below) but not regular bed files! Anyone have a good recommendation for ways to convert .bed to one of these file formats? Thanks!!! Lizzy Last edited by ewilbanks; 08-20-2009 at 12:10 PM. Reason: typo

08-21-2009, 01:25 AM	#2
dawe Senior Member Location: 45°30'25.22"N / 9°15'53.00"E Join Date: Apr 2009 Posts: 258	I guess you cannot go back to alignment data, because bed files only retain mapping positions (plus possibly some other information). You may do a couple of things: 1- simulate alignment data assuming all your reads are perfect matches with fake quality (possibly playing with awk and fasta reading tools) 2- try to fit your bed into the modified bed. Which "modified bed" format are we talking about? How do your data look like?