Comments (4)
Hi Chris,
We do a couple of different types of experiment here - one assumes knowledge of the input material - for this you simply make a reference containing all the sequences you wish to either include or exclude and compile a toml file accordingly - so lets say you have one species you wish to reject, define the whole of it's genome as a target and specify anything that matches to it to be rejected.
We have a second method - iteralign - which will fetch references from a database as it identifies them. This used centrifuge to identify reads and then grab the appropriate reference genomes.
Which sort of approach are you after?
Best
Matt
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I am making low input Rapid libraries using a phage lambda or T4 carrier DNA. The low input library is sometimes a human whole genome library. Sometimes it is a long human CATCH fragment (~1Mb).
I was think that to reject the off targets it might be more efficient to have mapping against both lambda and human references. This assumes that if an off-target sequence is mapped it can be rejected more quckly/efficiently - is that reasonable?
If this is a viable approach, I don't know how to set up such .mmi files. For instance, do I add a "chrL" to the hg38 ref fasta and make the minimap2 index from my "new" hybrid ref fasta?
from readfish.
To build your own reference, just cat together the two reference fastas and then build an mmi using the -d flag in minimap2 (see https://github.com/lh3/minimap2 documentation).
I think this should work. If you want to paste your toml file here once you've made it I'd be happy to look and see if it does what I think it should! It depends a little on the strategy you choose.
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Got it - thanks.
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