Re: [galaxy-user] SAM to GFF ?
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 the "BED-to-GFF converter" (Convert Formats) I hope this helps, Hans On 02/18/2011 01:22 PM, Peter wrote: 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 transcriptome mapping (RNA-Seq) for gene finding? Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] SAM to GFF ?
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 to GFF ? To: "Felix Hammer" Cc: galaxy-user@lists.bx.psu.edu Date: Friday, February 18, 2011, 8:09 AM 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 the mailing list. If you want to use the data in GBrowse then why not use SAM/BAM directly? I've not tried it yet but I understand GBrowse can display BAM files... best asking on their mailing list if you need more details. This doesn't involve Galaxy directly though... Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] SAM to GFF ?
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 the mailing list. If you want to use the data in GBrowse then why not use SAM/BAM directly? I've not tried it yet but I understand GBrowse can display BAM files... best asking on their mailing list if you need more details. This doesn't involve Galaxy directly though... Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-user] SAM to GFF ?
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 transcriptome mapping (RNA-Seq) for gene finding? Peter ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
