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-   -   Contig vs contig or map against contig lib? (http://seqanswers.com/forums/showthread.php?t=21111)

JackieBadger 06-24-2012 02:48 PM

Contig vs contig or map against contig lib?
 
Hi,

Can anyone offer some thought in regards to looking for SNPs between two sets of two EST contig libraries?

I have two cDNA contig libraries from sister species and wonder whether it is best to look for diagnostic SNPs between the two via BLAST/BLAT/BFASTing one contig set against the other, or assembling one of the species cDNAs against the contigs from the other?

I have already validated species level SNPs within each from the individual transcript assemblies. I am thinking the best way to look for species level SNPs would be to re-assemble the smaller sized data set against the larger contig library from the other species?

Aligning contigs against each other (in my mind) may cause more complications? (seeing as this is not an annotated scaffold).

Cheers,

J

jorge-bariloche 05-30-2016 05:34 AM

old question JackieBadger
 
Hi JackieBadger
Did you get some answer/solution/tip for this problem? I am more or less in the same situation
thanks


Quote:

Originally Posted by JackieBadger (Post 77141)
Hi,

Can anyone offer some thought in regards to looking for SNPs between two sets of two EST contig libraries?

I have two cDNA contig libraries from sister species and wonder whether it is best to look for diagnostic SNPs between the two via BLAST/BLAT/BFASTing one contig set against the other, or assembling one of the species cDNAs against the contigs from the other?

I have already validated species level SNPs within each from the individual transcript assemblies. I am thinking the best way to look for species level SNPs would be to re-assemble the smaller sized data set against the larger contig library from the other species?

Aligning contigs against each other (in my mind) may cause more complications? (seeing as this is not an annotated scaffold).

Cheers,

J



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