Question: Nanopolish variant calling. Need to specify input region of the reference genome
gravatar for Sudosundu
6 weeks ago by
Sudosundu0 wrote:

I mapped the reads with the reference fasta with minimap2. Out put: BAM file

Then I used the BAM, reference fasta, reads to nanopolish variant calling. And I got this error.

Error: genome has multiple contigs, please use -w to specify input region

My reference fasta contains 6 fasta sequences. It has no chromosome locations in it. Without knowing the chromosome locations (format: <chromsome_name>:<start>-<end>)) how do I specify the input region?

assembly genome • 93 views
ADD COMMENTlink modified 6 weeks ago by WouterDeCoster43k • written 6 weeks ago by Sudosundu0
gravatar for WouterDeCoster
6 weeks ago by
WouterDeCoster43k wrote:

Chromosomes are irrelevant. The tool looks at contigs regardless of how well assembled these are, and considers every sequence in your reference fasta a contig.

Say that you have the following fasta file:


Then -w my_fabulous_contig:2-5 would be perfectly valid.

ADD COMMENTlink written 6 weeks ago by WouterDeCoster43k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2225 users visited in the last hour