Question: Mapping using assembled contigs
0
gravatar for la_ff
7 weeks ago by
la_ff0
la_ff0 wrote:

Hi there, I have just downloaded some genome assemblies from NCBI that are assembled at the contig level, and they are in .fna format. From what I understand, after assembly into contigs, the next step in a genome analysis workflow is mapping back to where the contigs fit on the genome. I am using bbmap to do this. However, bbmap needs 'reads' as input files as well, and my files only have the assembled contigs in the .fna file. Do I need to redownload the raw reads to feed into this input? Or am I not understanding this workflow properly..

Thank you!

ADD COMMENTlink modified 7 weeks ago by colindaven2.3k • written 7 weeks ago by la_ff0

Not quite. That mapping back is done only if you created the contigs yourself from raw sequence data. What exactly are you trying to do?

ADD REPLYlink modified 7 weeks ago • written 7 weeks ago by genomax85k
1
gravatar for colindaven
7 weeks ago by
colindaven2.3k
Hannover Medical School
colindaven2.3k wrote:

The contigs ARE the (poor estimation or build of) the genome. You won't get further information by mapping them back to a related genome. You might want to only work with properly assembled (finished, complete) genomes.

ADD COMMENTlink written 7 weeks ago by colindaven2.3k
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