newbie question: mapping solid reads

[crh]

Hi,

I have no experience mapping nextgen sequences back to ref genome, so please excuse my ignorance.

A colleague has generated some SOLID transcriptome sequences and has asked me to map them to the genome. I'm at an undergrad institution, but we have a good server setup that should handle the task.
I've looked through the site here and see people using maq, bowtie ...mapreads.

I'm hoping for help on building an analysis pipeline that will enable us to map the reads, visualize the results on a browser (gff) and get some quantitative dat - % mapped.

Just to see if I could get the reads to amp I took 1 set (cell) and ran mapreads:
mapreads ../xxxx.csfasta references/Chlre4_genomic_scaffolds.fa Q=../xxxxxx_QV.qual I=1 >mapreads.out

I have not tried to quantify the %mapping yet, but estimate 10-20%max.

Any suggestions re: software, parameters, etc appreciated

Charles

[mrawlins]

My Experience

We've been using BioScope, which is relatively slow on a 48-processor cluster, and it's giving us good results. The previous version of their mapping tools are available under the GPL at http://solidsoftwaretools.com/ . There is read mapping (which has a summary including the % of reads mapped) as well as junction mapping and exon counting, which takes care of splicing (alternative and not) and/or transposons and results in semi-quantitative results for each gene.

For visualization I would use IGV, Tablet or MagicViewer.

-Mitch

[westerman]

mapreads is part of both Bioscope and the older Corona Lite suite. I agree that using Bioscope gives good results for transcriptome projects. So if you are not using it then I suggest converting to it.

[crh]

Thanks for the advice, we'll give it a try.

Charles