rhemac8

[Todd Bradley]

Could the Rhesus macaque genome release 8 (Rhemac8) be added as a supported genome on the IGV browser? Thanks!

[Jim Robinson]

Hi, this has been added.  Apologies for the delay.

[Todd Bradley]

Thanks! However, now I'm getting an error that the names don't match in my bam file. I check the bam file and the chromosome names do not have the prefix "chr" Could you add that alias to this genome?

[James Robinson]

Aliases 1 <-> chr1,  etc, are built in for all genomes, including this one.

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[Todd Bradley]

Hi,

I still can't get my bam files to load on this genome. They load on rhemac3 but the reads don't align with the gene. When I try to load the same .bam file on rhemac8I get the error below:

File: /Volumes/dusom_dhvi/DHVI_Illumina/Rhesus_FC/BAM/1259Aligned.sortedByCoord.out.bam
does not contain any sequence names which match the current genome.

File:      1, 2, 3, 4, ...
Genome: chr1, chr2, chr3, chr4, ...     

I used sametools to view the bam file and below is the beginning of this file. I see that the names are 1, 2, etc. Any other thoughts how to get this to work? Thanks!

@HD VN:1.4 SO:coordinate

@SQ SN:1 LN:225584828

@SQ SN:2 LN:204787373

@SQ SN:3 LN:185818997

@SQ SN:4 LN:172585720

@SQ SN:5 LN:190429646

@SQ SN:6 LN:180051392

@SQ SN:7 LN:169600520

@SQ SN:8 LN:144306982

@SQ SN:9 LN:129882849

@SQ SN:10 LN:92844088

@SQ SN:11 LN:133663169

@SQ SN:12 LN:125506784

@SQ SN:13 LN:108979918

@SQ SN:14 LN:127894412

@SQ SN:15 LN:111343173

@SQ SN:16 LN:77216781

@SQ SN:17 LN:95684472

@SQ SN:18 LN:70235451

@SQ SN:19 LN:53671032

@SQ SN:20 LN:74971481

@SQ SN:X LN:149150640

@SQ SN:Y LN:11753682

@SQ SN:MT LN:16564

@SQ SN:KQ739485.1 LN:919841

@SQ SN:KQ739657.1 LN:805525

@SQ SN:KQ732613.1 LN:643885

@SQ SN:KQ733369.1 LN:610816

@SQ SN:KQ742746.1 LN:602698

@SQ SN:KQ732984.1 LN:576867

@SQ SN:KQ734207.1 LN:516943

@SQ SN:KQ737751.1 LN:471937

@SQ SN:KQ738522.1 LN:469061

@SQ SN:KQ737594.1 LN:416698

@SQ SN:KQ737037.1 LN:376070

@SQ SN:KQ740843.1 LN:368708

On Friday, June 23, 2017 at 9:31:44 PM UTC-4, Jim Robinson wrote:

Aliases 1 <-> chr1,  etc, are built in for all genomes, including this one.

On Fri, Jun 23, 2017 at 5:04 AM, Todd Bradley <toddcb...@gmail.com> wrote:

Thanks! However, now I'm getting an error that the names don't match in my bam file. I check the bam file and the chromosome names do not have the prefix "chr" Could you add that alias to this genome?

On Thursday, June 22, 2017 at 5:18:04 PM UTC-4, Jim Robinson wrote:

Hi, this has been added.  Apologies for the delay.

On Tuesday, June 6, 2017 at 11:20:04 AM UTC-7, Todd Bradley wrote:

Could the Rhesus macaque genome release 8 (Rhemac8) be added as a supported genome on the IGV browser? Thanks!

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[James Robinson]

That should work.  I assume you're using a recent release of IGV, but you didn't say.  What release are you using?

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[Todd Bradley]

I am using IGV 2.3. Should I be using the beta 3.0?

[James Robinson]

OK I made some progress on this.  The auto-alias code had a limit of 10,000 chromosomes (contigs),  after that it didn't try.   This fasta has ~28,000 sequences in it.   

So this is an easy fix, but there is more than 1<->chr1 to match, in particular chrX, chrY, and chrM.   Do you know how these are named in your bams?  Actually could you point me to the fasta these bams are aligned to?    

Its quite easy, BTW, to make an alias table yourself.   I'm happy to do it for the benefit of others but need the mappings or fasta.

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[James Robinson]

Correction, 284,728 sequences.

[Todd Bradley]

Hi Jim-- the fasta was downloaded here: http://www.ensembl.org/Macaca_mulatta/Info/Index. To align these bams I used "Macaca_mulatta.Mmul_8.0.1.dna.toplevel.fa" Thanks so much for your help with this.

Best,

Todd

Correction, 284,728 sequences.

[James Robinson]

This should work now, but you will need to delete rheMac8.genome from the igv/genomes folder to force an update.