Sam To Gff ?

Question: Sam To Gff ?

7.8 years ago by

Felix Hammer • 200

Felix Hammer • 200 wrote:

Hi, is there an easy way to use Galaxy to convert SAM to GFF? thx, Felix

gff • 2.7k views

ADD COMMENT • link •

modified 3.0 years ago by h.stotz • 20 • written 7.8 years ago by Felix Hammer • 200

7.8 years ago by

Peter • 30

Peter • 30 wrote:

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

ADD COMMENT • link written 7.8 years ago by Peter • 30

Hi Felix It might be a little bit unusual to use the "generic feature format" (GFF) to show where your reads map....but 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

ADD REPLY • link written 7.8 years ago by Hotz, Hans-Rudolf • 1.8k

7.8 years ago by

Peter • 30

Peter • 30 wrote:

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

ADD COMMENT • link written 7.8 years ago by Peter • 30

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. Subject: Re: [galaxy-user] SAM to GFF ? To: "Felix Hammer" <hammerf@cip.ifi.lmu.de> Cc: galaxy-user@lists.bx.psu.edu Date: Friday, February 18, 2011, 8:09 AM 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/

ADD REPLY • link written 7.8 years ago by vasu punj • 360

3.0 years ago by

h.stotz • 20

European Union

h.stotz • 20 wrote:

I am trying to use cufflinks, but it does not recognise my reference annotation. I have a gff3 flile in my history. So, it should be recognised. The fasta file on the genome has been uploaded and covers all of the genome sequence. I notice that there is a run of NNNNNNNNs at the beginning of the first chromosome. Would that cause problems?

Thanks,

Henrik

ADD COMMENT • link written 3.0 years ago by h.stotz • 20

Please log in to add an answer.

Similar posts • Search »