Mapping of SOLiD reads

[JohanS]

Hi. I have a small question about mapping small SOLiD reads against a reference library of small sequences. I'm using Bowtie at the moment and i notice that i get a lot of coverage in the middle of the reference sequences but no coverage at the ends.

My wish is to obtain coverage over the whole sequence and also to obtain information about reads that align partly to a sequence e.g half of the read aligns to the reference sequence. As i understand it it is not possible to achieve this with Bowtie ?

Is there any other aligners that can do this (in colorspace that is) ?

Regards
Johan

[colindaven]

Perhaps Novoalign CS might be better. I don't know if the CS version is free, I think not. If I recall correctly you can set it to automatically trim reads to get alignments.

Is it possible to extend your reference sequences so that bowtie can map to them ?

Are we talking genome, transcriptome ... ?

[Marcos Mota Costa]

Solid software request

I am trying to download Corona Lite and csfasta_quality_filter.pl from solidsoftwaretools.com. But I don't receive the confirmation email in order to complete the registration.
Could someone send me those packages or place somewhere I could download? (The license is GPL).

Thanks.