mapper which work with ambiguous bases

[dietmar13]

hello,

which (RNA-seq) mappers can use ambiguous bases in the reference genome?
-STAR
-subread
-RUM
-tophat


ambigous bases are e.g.
W for A,T
S for G,C
Y for C,T
B for non-A
...

and is there a script which can use a SNP dataset and modify the genome accordingly: replace all SNP positions with the correct ambiguous bases?

dietmar

[gringer]

Tophat/Bowtie works with 'N' (i.e. any base), and I think any non-ACGTU are converted to Ns. To accept all ambiguous bases in a DNA database, you need to double the minimum number of bits used to 4 (i.e. presence/absence of each base). The search algorithms also need to change quite a bit, which will probably at least double the time taken. I'm not yet convinced the added complexity is worth it.

[dpryan]

Gsnap can map to a genome with SNPs though I don't think it takes the exact input type you have in mind.