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
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
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