LASTZ Multiple Alignment File (MAF) visualization

[Milo Z]

Hello,

I have completed a pairwise alignment of two de novo plant genome assemblies to a reference genome separately using LASTZ. Then I used MULTIZ to combine the alignments to a MAF file. I would now like to visualize the MAF file on Circus. Can you please assist me on this task? I have the annotation of the reference genome on a GFF file as well as its fasta file, and the MAF file. I would really appreciate your help.

Thank you,

-Milo

[Martin Krzywinski]

You'll need to parse the MAF alignment file to obtain alignment positions in a format like

chr1 start1 end1 chr2 start2 end2

You'll need the chromosome structure of the reference genome along with the assembly. If the assemblies are not anchored to chromosomes (e.g. 1000s of contigs), you'll probably need to concatenate the contig positions so that the position is now relative to the entire assembly rather than to each contig. 

While you could draw all the contigs from each assembly as a "chromosome", this isn't very practical once you get into 1000s of contigs -- the size of each contig would be the size of a pixel on an image and too small to see in print.

M

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

--
You received this message because you are subscribed to the Google Groups "Circos" group.
To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visual...@googlegroups.com.
To post to this group, send email to circos-data-...@googlegroups.com.
Visit this group at http://groups.google.com/group/circos-data-visualization.
For more options, visit https://groups.google.com/d/optout.

[Milo Z]

Hi Martin,

So I can convert the MAF file to BED. Would BED format work as input? Please let me know.

Thank you,

Milo

On Thursday, October 8, 2015 at 7:39:35 PM UTC-4, Martin wrote:

You'll need to parse the MAF alignment file to obtain alignment positions in a format like

chr1 start1 end1 chr2 start2 end2

You'll need the chromosome structure of the reference genome along with the assembly. If the assemblies are not anchored to chromosomes (e.g. 1000s of contigs), you'll probably need to concatenate the contig positions so that the position is now relative to the entire assembly rather than to each contig. 

While you could draw all the contigs from each assembly as a "chromosome", this isn't very practical once you get into 1000s of contigs -- the size of each contig would be the size of a pixel on an image and too small to see in print.

M

Martin Krzywinski

science + art

http://mkweb.bcgsc.ca

On Tue, Sep 15, 2015 at 5:54 PM, Milo Z <chit...@gmail.com> wrote:

Hello,

I have completed a pairwise alignment of two de novo plant genome assemblies to a reference genome separately using LASTZ. Then I used MULTIZ to combine the alignments to a MAF file. I would now like to visualize the MAF file on Circus. Can you please assist me on this task? I have the annotation of the reference genome on a GFF file as well as its fasta file, and the MAF file. I would really appreciate your help.

Thank you,

-Milo

--
You received this message because you are subscribed to the Google Groups "Circos" group.

To unsubscribe from this group and stop receiving emails from it, send an email to circos-data-visualization+unsub...@googlegroups.com.

[Matt Simenc]

Here three Python 3 scripts for making Circos files you might be able to use. The gff2tile script makes a feature for a tile track for every feature in a GFF3 file. The gff2heatmap script bins up features from each scaffold/sequence in a GFF3 file into a bin size you choose with -window into a heatmap style track, and the fasta2GC script makes a heatmap style track for GC content from a FASTA file.

[Matt Simenc]

If you run the scripts with no arguments it should show a help

[Matt Simenc]

Previous script had a bug- here's an updated version that works.