Question: Minimap2 warning message
0
gravatar for KVC_bioinfo
2.6 years ago by
KVC_bioinfo440
Boston
KVC_bioinfo440 wrote:

Hello,

I am using Minimap2 for the Oxford nanopore reads. I made an index file for the human genome to be used as a reference. when I started the alignment I got following warning.

"For a multi-part index, no @SQ lines will be outputted"

I am not sure why I am getting this warning. Could someone help me here?

Thank you in advance.

ont aligner minimap2 • 2.0k views
ADD COMMENTlink modified 2.5 years ago • written 2.6 years ago by KVC_bioinfo440
1

Please be as complete as possible when asking questions, and include the commands you used for building the index and running the alignment.

Also, don't forget to follow up on your previous questions and mark answers as accepted if it solves your question.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by WouterDeCoster43k

Thank you I have added the comment here with my command and I also took follow up on my past questions.

ADD REPLYlink written 2.6 years ago by KVC_bioinfo440

The command I used for building index:

minimap2 -d ref.mmi ref.fa

The command I used for alignment:

minimap2 -ax map-ont ref.fa ont-reads.fa > aln.sam

ADD REPLYlink written 2.6 years ago by KVC_bioinfo440

Hello Please i want to know what that mean map-ont ??

ADD REPLYlink written 5 weeks ago by Bioinfo20

It's a preset combination of alignment parameters which the developer thought was the best for ONT data

ADD REPLYlink written 5 weeks ago by WouterDeCoster43k
1
gravatar for KVC_bioinfo
2.6 years ago by
KVC_bioinfo440
Boston
KVC_bioinfo440 wrote:

I have got help from the authors of minimap2. I downloaded the reference from here which is very confusing. when Replaced the reference with this Minimap2 works fine.

ADD COMMENTlink written 2.6 years ago by KVC_bioinfo440
1

For future reference, see this thread https://github.com/lh3/minimap2/issues/58

ADD REPLYlink written 2.5 years ago by WouterDeCoster43k

Thank you for putting the reference here.

ADD REPLYlink written 2.5 years ago by KVC_bioinfo440
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