Problems with bacteria_tradis mapping about bio-tradis HOT 1 OPEN

Hi,

First, I would try to follow the tutorial exactly, e.g. using smalt and not trimming tags yourself:

https://github.com/sanger-pathogens/Bio-Tradis/blob/master/BioTraDISTutorial.pdf

BWA has some problems with mismapping, as it will soft-clip reads leading to a lot of incorrect read assignments, so I would avoid using it. I've also never used the tagless mode, this was added later, so I don't know how this might affect the mapping.

If you're still getting low mapping rates, I would try A) using FastQC to check that you don't have some obvious problems (e.g. additional adapter contamination, low quality, weird over represented sequences), B) BLAST some of your reads against the reference genome and through NCBI BLAST to see if they actually do match your reference genome, or if not what the source might be. Depending on how the libraries were made, potentially this could also arise from something like a delivery vector, e.g. if you're conjugating in a plasmid with the transposon on it and it hasn't been properly cleared.

Let me know if this helps.

-Lars

from bio-tradis.