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mcfrith / last-rna

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How to visualize output from the long reads tutorial #2

Open lfaller opened 6 years ago

lfaller commented 6 years ago

Hi all,

I have Minion data for two closely related microbial strains. I assembled the two strains into two assemblies of four and five contigs.

I then followed your notes regarding using LAST to align long reads (https://github.com/mcfrith/last-rna/blob/master/last-long-reads.md)

Now I have a .maf file, but I can't seem to visualize it with either Geneious or IGV.

Do you have suggestions for how I can visualize the MAF file? I am used to dealing with VCF format, but I have not been able to convert the MAF file that LAST produces.

Thanks for any advice! ~Lina

mcfrith commented 6 years ago

Hi Lina,

perhaps you can use last-dotplot to visualize.

Alternatively, you can use maf-convert (which is in the LAST package) to convert maf to some other alignment format.

Note that vcf is not an alignment format: going from alignments to vcf is a nontrivial process. I have no particular suggestions for doing that, but someone else may do.

Have a nice day, Martin

lfaller commented 6 years ago

Thanks for the feedback, Martin!

I tried the dotplot visualization and while it gives a nice birds-eye view, I am hoping for a solution that let's me look a bit closer.

Cheers, ~Lina

mcfrith commented 6 years ago

Hi Lina

I'm mostly out of ideas...

last-dotplot has options to increase width/height, or select sequences or parts thereof. But I guess you want an interactive viewer.

I'm not sure what your alignments are of (contigs versus contigs? reads versus contigs?) which seems important for this question.

You could try asking somewhere like biostars.org.

Have a nice day, Martin