search

DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
187 stars 44 forks source link

Mapping file advice #40

Closed ptranvan closed 7 years ago

ptranvan commented 7 years ago

Hi,

First I would like to produce a mapping file for coverage estimation and then plot a blobplot.

For removing contaminations, I will select the contigs that have been assigned to the desire organisms and mapped my initial reads to those contigs.

Do you have any advice for the mapping file (parameter etc.)?

I'm using bwa mem but I'm wondering whether I should use the -m option (discard reads mapping to multiple locations)

DRL commented 7 years ago

Hi ptranvan,

Blobtools uses only reads that pass the following samflags

samtools view -f 1 -F 1024 -F 256 -F 2048

so you shouldn't have to worry about multimappings .