Im sitting with several thousands abi-files/chromatograms that need be located onto the mouse genome.
I would be very greatful to any who can tell me a way to speed up the process (i have the feeling that the Staden package can help me, at least partially - it must be a common 'problem' to many - but im rather newbee in the bioinformatics).
I need to do the following:
1) remove some vector sequence
2) identify the insert orientation (from the sequence of step 1))
3) align to the murine genome
4) retrieve results
In advance: thanks
Removal of vector can be achieved using Pregap4's vector_clip module or via cross_match. Crossmatch is a blunt instrument, but simpler to use.
For mapping against the genome, to be honest I'd say something like ssaha2, blast, blat, etc (a quick google should help find them) is a quicker route, or cross_match again.
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