Mapping of reads (phyluce_snp_bwa_multiple_align)

faircloth-lab / phyluce

software for UCE (and general) phylogenomics

http://phyluce.readthedocs.org/

Other

78 stars 49 forks source link

Mapping of reads (phyluce_snp_bwa_multiple_align) #288

Open irbinveliz opened 1 year ago

irbinveliz commented 1 year ago

Hello, I am trying to map my trimmed reads to a pseudo-reference sequence. I have seen that for phyluce versions 1.4 and 1.5 this was done using the snsp.py script and I have also seen that there used to be a function called phyluce_snp_bwa_multiple_align which allowed you to do that. However, I am running phyluce version 1.7.1 and I am not able to call that function. Thank you in advance for your help.

brantfaircloth commented 1 year ago

Hi Irbin,

Slightly different procedures for this exist now. You should be able to modify what is explained here to suit your purposes.