Hi Felix
It might be a little bit unusual to use the "generic feature format"
(GFF) to show where your reads mapbut strictly speaking mapped reads
on a genome are 'features' as well.
You can do it the following way:
first use the "Convert SAM to interval" tool (NGS: SAM Tools), and use
I have used IGV with the Bam file and one ha sto generate index file which can
be done in IGV, it work well. Gbrowser should also be OK. I think new version
of IGV provide lot more features than previous one
Vasu.
--- On Fri, 2/18/11, Peter wrote:
From: Peter
Subject: Re: [galaxy-user] SAM
On Fri, Feb 18, 2011 at 12:35 PM, Felix Hammer wrote:
>
> Hi Peter,
> thx for the reply.
> You're right I want to display mapped RNA seq data in gBrowse.
> Currently I have the data in SAM format.
> Maybe I can figure out a trick using the text manipulation tools.
> thx,
> Felix
You forgot to CC
On Fri, Feb 18, 2011 at 12:08 PM, Felix Hammer wrote:
> Hi,
> is there an easy way to use Galaxy to convert SAM to GFF?
> thx,
> Felix
How so?
SAM/BAM shows you where your reads map, GFF is used for
annotation (e.g. where the genes are and what they may do).
Are you talking about using SAM/BAM
4 matches
Mail list logo
