Alignment SOLID data

[lellabioinfo]

Dear users,
someone knows how I can align multiple microRNA reads in gff format?
Is it possible (and, if yes, how) with SOLID ALIGNMENT BROWSER?
Thanks a lot

[westerman]

Dear users,
someone knows how I can align multiple microRNA reads in gff format?
Is it possible (and, if yes, how) with SOLID ALIGNMENT BROWSER?
Thanks a lot

The Browser merely allows you to see pre-computed alignments so the answer would be "no, you can not align using SAB."

I am still working with my first microRNA sample and thus my advice may not be correct. That being said, having your microRNA reads in GFF format indicates that you have already run the color-space SOLiD reads through a program. Presumably rna2map. Thus you already have the alignment. I would assume that the file could be viewed via the SAB.

If the above is not useful then perhaps you could restate your question.

[lellabioinfo]

Dear Westerman, you are right: my question is not so clear!
I have csfasta (and QV) data from RNA of different patients. To find mutations among these files, what software or tool can I used? I need a multiple alignment browser. Because of these csfasta contains all the transcriptome, how can I select only microRNA?
Thanx a lot for your help!

[westerman]

Once again I have not completed a microRNA project using SOLiD data (we are having problems with our reference sequence) but what I would do is run each of your data sets through the rna2map program. Then using the results from that program see where the differences are in your data.

I don't see where a graphical alignment browser will help since you will undoubtedly be dealing with hundreds if not thousands of differences. Plus the differences are on parts of the genome that are widely separated from each other. You might be able to use a clustering program such as those used in microarrays to determine clusters of microRNAs and graphically display these clusters.