sequence capture visaulization

[litali]

Hello all
Does anybody know if there is a graphical solution to see the results of a sequence capture experiment. For example to see the targets and which regions were covered and to see the variations comparing to a reference file etc..
Thank you!!!

[ulz_peter]

Hi litali,

That depends on the file formats you have. If you've got the target regions in .gff or .bed and the alignment in .bam (with associated index file) you could go for the UCSC Browser (if the alignment file is large, what it usually is you will need a web-accessible server to store the data there).
Another options is Tablet, accepting BAM and GFF input.

For proper help I would need more information...

Regards,
Peter

[litali]

seq cap

Thank you for your reply. I have .ace format. I also have the capture regions, but not in a gff format but just like a list: chr1: x-y
chr2:x-y
etc
I also havethe reads in raw fasta format...
Thanks alot!

[ulz_peter]

Hi litali,

The Tablet manual says it can visualize .ace files as well (I never tried that though...)

Tablet is available under:

http://bioinf.scri.ac.uk/tablet/index.shtml

Reformat your list into GFF like described at the UCSC homepage:

http://genome.ucsc.edu/goldenPath/help/customTrack.html#GFF

(you will need a script written in perl or python to do this, if you've got lots of regions...)

I hope this helps...
(BTW: Is your output from the Roche Software? I wonder why they haven't implemented SAM/BAM output yet...)

Best regards,
Peter