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Old 06-21-2010, 07:51 AM   #1
crh
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Default map solid reads to ncRNA database

Hi,

I'm interested in mapping solid reads to a database of non-coding RNAs (miRNA etc).

If I could convert the color-space data to DNA sequence I would consider using blat or blast.
Does a tool exist for conversion color-space->DNA?

Any suggestions for a good mapping tool/strategy for this?
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Old 06-21-2010, 09:10 AM   #2
epigen
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Default Do not convert color-space data to nucleotides before mapping!

Some useful threads about the color space to nucleotide issue:
http://seqanswers.com/forums/showthread.php?t=2312
http://seqanswers.com/forums/showthread.php?t=2226

and about miRNA mapping:
http://seqanswers.com/forums/showthread.php?t=2182

ABI's SOLID analysis toolbox, BioScope, provides an easy-to-use interface but installation is a bit tricky (does not work properly on a cluster with CPUs distributed over several nodes). Pre-BioScope tools are available open source.
Other software is command-line only but has better user support. The developers are active on this forum. If you have limited computational equipment, you might consider Bowtie. It can be run on a normal PC and is very fast, but it does not align with indels. Otherwise, if you want a fast mapping tool with indels, I'd recommend BWA. There are also BFAST and NovoalignCS, which are slower but may be more sensitive because they align in real color space. (For BWA, the reads have to be pre-processed with its solid2fastq script, converting color space codes 0123. into ACGTN for alignment purposes. This is somewhat confusing because unaligned reads are reported in this pseudo-nucleotide code whereas aligned ones are converted into real DNA sequences.)
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Old 07-19-2010, 12:22 PM   #3
aguffanti
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Default miRNA mapping

Hi - I would use SHRiMP from M.Brudno's group to map SOLiD reads against miRNA db. It is slow but it does contain a 'miRNA' specific mode

Kind regards,

Alessandro
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