Question: Mapping to custom reference minimap2/IGV
0
gravatar for sendhelp
15 months ago by
sendhelp0
sendhelp0 wrote:

I'm trying to map nanopore reads to a mtDNA reference using minimap2 for the purpose of determining how many mitochondrial reads are present in the nanopore data.

The minimap command I'm using is;

~/apps/minimap2/minimap2 -ax map-ont mtref.fa reads.fq  > aln.sam

I know there are mtDNA reads present as I can align them to the reference, however when I look at the resulting indexed and sorted sam file in IGV there's no coverage?

Thanks!

igv nanopore mapping minimap2 • 854 views
ADD COMMENTlink modified 15 months ago by genomax91k • written 15 months ago by sendhelp0

Have you made a custom genome in IGV using the same reference? By default IGV shows you the entire reference so you may need to zoom in before you start seeing the reads.

ADD REPLYlink written 15 months ago by genomax91k

I have. I solved the initial problem by actually creating a sorted bam file and using that in IGV rather than just the same file. Thanks!

ADD REPLYlink written 15 months ago by sendhelp0
1
gravatar for ATpoint
15 months ago by
ATpoint40k
Germany
ATpoint40k wrote:

You can simply check the full alignment using samtools idxstats for the number of reads mapping to chrM.No need to align against a specific subset (which is also not recommended).

ADD COMMENTlink written 15 months ago by ATpoint40k

Thank you! Can I ask why it isn't recommended to align against a subset (I think you're referring to aligning genomic reads to a single chromosome reference?)

ADD REPLYlink written 15 months ago by sendhelp0
1

The aligner will always try to find the best match for each read in the library. If your library contains reads from the entire genome but you include only one chromosome (or one region) with the true origin of the read missing the aligner might false-positively put it somewhere else. I never quantified what the extend of false-positives is but this opinion is pretty much what I read here at Biostars from many of the more experienced folks.

ADD REPLYlink written 15 months ago by ATpoint40k

Ah, makes sense! There isn't a reference genome available for me currently so I guess this is the only method?

ADD REPLYlink written 15 months ago by sendhelp0
1

Well I am spoiled by working with mouse and human only (and I often forget that when writing answers :-D ) but yeah if you have no reference I would include as much of the draft genome or the contigs you have and then filter for the regions/contigs/chromosomes you need.

ADD REPLYlink written 15 months ago by ATpoint40k
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