[nilshomer]

Hi. everyone.

Should we transform the fastq file from solid2fastq (Bfast) before mapping with bwa?
I mean from "0123123" to "ACTGACT", something likewise plus some other format issues?

Before, I proced without any transformation, then got malformed .sai file and some "segmentation fault" which I haven't specified yet.

Any suggestions? Thank you

Make sure you use the solid2fastq within BWA if you are going to use BWA. On the other hand, if you are using bfast+bwa, make sure you see the command line parameters in BFAST's solid2fastq.

[nilshomer]

I'm wondering in the postprocess step, if BFAST will do something like: choose the best for F and second best for R within a pair because that is within the expected distance, yet the best for R is in another chromsome.
I know it is a rare scenario and maybe I should not worry about it.

It could happen when using the insert size distance in the probability calculation, though it is rare.