rnaspades output: contigs coverage

Question

[xuling2015]

Hi Everyone,

I'm using rnaspades to assemble my metatranscriptome data. In output folder, I didn't see any reads count file(How many reads mapped to each contig). There is no sam file too. I need to know coverage information for each contig. Does anybody know what's going on here?

Thanks a lot!

Jasmine

Answer 1

[Asaf]

You can re-map the reads to the contigs and get the coverage.

Answer 2

[yangchengzhong518]

But how? What kind of software should be used?