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rnaspades output: contigs coverage

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

rna-seq
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updated by yangchengzhong518 • yangchengzhong518 • written by xuling2015 • xuling2015

2 answers

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

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written by Asaf Asaf

But how? What kind of software should be used?

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written by yangchengzhong518 • yangchengzhong518

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