Convert SAM to GFF

[Darwin]

Hi,

Does anyone know of an easy way to convert files in the SAM format to GFF (or GFF3)?

I do RNA-seq and have my output from tophat that I'd like to visualize on gbrowse (v1.7), which as far as I can tell does not support SAM. I know I could upgrade to Gbrowse2, haven't got the courage just yet..

Any help is appreciated,
Darwin

[kmcarr]

Do not try to use GFF for Next Gen sequencing data. You will melt your cpu into a smoking pile of ash. O.K. not really; truth is you browser will time out before GBrowse ever returns.

GBrowse 1.7 can use the Bio:B::SAM backend. See the poster at this link.

But really, make the switch to GBrowse 2.0. It is now very easy to install; you install both BioPerl 1.6 and GBrowse 2 through CPAN. Configuring multiple data sources for a single browser makes life much easier.

[Darwin]

Thanks for the reply.

I'm a bench biologist just getting my toes wet on the command line and so prefer to keep it as uncomplicated as possible. But I think you're right that there's a shiny new GBrowse in my future.

Have you or anybody else installed GBrowse2 on OS 10.6 or would I need to set up a virtual ubuntu box? It took me *a while* to install GBrowse 1.7 on this system hence my hesitation to switch.

[kmcarr]

Thanks for the reply. Have you or anybody else installed GBrowse2 on OS 10.6 or would I need to set up a virtual ubuntu box? It took me *a while* to install GBrowse 1.7 on this system hence my hesitation to switch.

The more times you install BioPerl and GBrowse, the faster you get at it .

I have installed GBrowse on my Mac which is running 10.5. When installing on a Mac the thing to remember is that the standard locations for the web browser document and cgi-bin directories are different from the standard Linux locations. You will need to know these locations when you are configuring GBrowse on your Mac.

Also, if you are installing via the CPAN shell, make sure to set the shell to 'verbose', otherwise you will not see the configuration queries and it will appear that the install is stalled. This is true for both Mac and Linux.

[steven]

If you are not limited to GBrowse, you may be interested in trying other browsers (IGV, IGB, CisGenome, etc). A lot of them load SAM/BAM files directly. You can find more info in this thread for instance.

[Darwin]

I would like to stay on GBrowse because is seems versatile (can host all sorts of genomic features) and that's where I have accumulated whatever experience that I now have.

IGV does look fairly easy to setup so I'll keep that in mind.

Thanks for your help guys!

[neXtGen seq]

Sam to gff3

Darwin. Have you found a way to convert sam files to gff3. if so please share

i HAVE INCLUDED MY EMAIL INCASE YOU WANT TO SEND IT TO MY EMAIL [email protected]

[sagarutturkar]

SAM to GFF

Have anybody figure out how to convert SAM to GFF? Please share.

[arvid]

GBrowse supports BAM nowadays, so I don't quite see the need... But it should be quite easy to write a converter (e.g. in Perl or Python), depending on which fields you wish to keep. A good exercise for learning a scripting language!
Otherwise you can convert the SAM to sorted BAM, use the BAM to BED converter in BEDTools, and convert BED to GFF in Galaxy...