Re: c.elegans WS235 genome

[kirill....@monash.edu]

Hi there,

I need to work on c.elegans WS235 genome. The bam and tdf file have came from the raw reads alignment to the WS235 genome (not by me). I have tried to import new genome myself but it doesn't work, can't see genes only the sequence.
I went File > Import Genome and only loaded two files 1. fasta and 2.GFF. Both files were downloaded from the wormbase.org repository at ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/. Here are names of the two files c_elegans.WS235.annotations.gff3.gz, c_elegans.WS235.genomic.fa.gz. I have gunziped the fasta file before loading it in.

I either need a ready to go WS235 genome for IGV or a bit more explanation on what am I doing wrong (preferred, please).

Many thanks in advance

Kirill

[Jim Robinson]

Hi Kirill,

Apologies for the delayed response.  You didn't say how the genome import failed, but I suspect problem with that gff file is its size, it is too large to load as part of the "genome".    For cases like this I suggest you do not include the gff file in your genome definition,  instead just gunzip and load the fasta file.  For the gff use igvtools to index the file and load it separately.   You can do this from the IGV UI (in the Tools menu),  or the command line.   If the gff is not sorted by position you will need to sort it first.

Also, see if the gff has a fasta section at the end.  If it does you will want to remove it.

I've made a note to add this genome to our hosted list.  Before doing this I will strip all non-gene features from that gff to get it to a manageable size.  

Jim

[kirill....@monash.edu]

Hi Jim, thank you for your answer. I seems that now I have functional WS235 genome loaded into IGV. Before I was trying to load full GFF file downloaded from wormbase, that included features such as SAGE_tag and SNP's and it probably was too big. There was no error message. The IGV simply didn't show any genes positions, just the sequence. I wasn't sure what are the main features from GFF needed for IGV to display genes position correctly. Your previous answer have helped me. I have curated another GFF that has gene, mRNA, exon and intron features only. I have sorted it using igvtools and then indexed it. I loaded both new GFF and fasta files using import genome in the file menu. Except I didn't load indexed GFF file anywhere. I have kept it in the same directory as the genome file. Is it right? It works. I can see the sequence and genes location.

To others: I had problem creating sorted GFF file using UI igvtools. Error type: Unknown file type. Because I was loading GFF file with the file extension .gff3 when i renamed it to .gff it worked straight away.  

Cheers

Kirill

[Richard Mott]

Hi Kirill

I have the same issue regarding WS235

Would you mind telling me precisely which features you extracted from the WS235 gff3 annotation file ? For example there are several "gene" types, and I'm not sure which one IGV wants

Thanks

Richard Mott

[Jim Robinson]

Hi Richard,

Below is a list of feature types we extract for building a "gene" annotation file.   The list represents types we've seen in various gff like files, for gff3 you will only see a subset of these.   Hope this is helpful.

Jim

five_prime_UTR
5'-UTR
5'-utr
5UTR
three_prime_UTR
3'-utr
3'-UTR
3UTR
CDS
cds
exon
coding_exon
intron
transcript
processed_transcript
mrna
mRNA

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[Richard Mott]

Hi Jim

thanks very much

I also found that the chromosomes are named differently in the worm base annotation gff compared to the worm base fa (e.g. "CHROMOSOME_V" instead of "V"). Once I fixed that I could import the annotations

Richard

[bw9...@bristol.ac.uk]

Dear Jim,

I am considering realigning my genomes from WS220 to WS245 which is the current C elegans release.  Are there any plans to add WS245 to the genome list? This might be especially helpful now the latest wormbase tools such as WormMine do not support WS220.

Best wishes
Barney

[Jim Robinson]

Hi,

We add genomes on request, if the data is public. I need urls to the
files, either fasta or genbank format + annotations (usually gff).

Jim

[SM Pyonteck]

Hi Jim,

I am also working on C. elegans and would sincerely appreciate if the WS245 version of the genome was available in IGV. I have included a link to the FTP site which contains the genome and annotations here:

ftp://ftp.sanger.ac.uk/pub/wormbase/FROZEN_RELEASES/WS245/species/c_elegans/PRJNA13758/

Thank you for your help! Much appreciated!

All the best,

Stephanie

[Jim Robinson]

Hi,

This is now available.  The annotation file had to be trimmed significantly, it's 3.5GB uncompressed.  I grepped out all the wormbase annotations, so what you'll see when you load it are those.  If you are interested in the entire file you will need to download it,  gunzip it, then index it with either tabix (best) or igvtools.  After doing this you can load it from the file menu.

[SM Pyonteck]

Hi Jim!

This is fantastic and a HUGE help to me! Thank you so much for taking the time out of your busy schedule to prep this! I sincerely appreciate it! Thanks again!

Best wishes,

Stephanie

[Barney Wharam]

Dear Jim,

Thank you so much, I had forgotten about this, but it will be useful over the coming months. IGV is an amazing tool!

Best wishes

Barney

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Barney Wharam

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Nematode Biology (Lab: 245, 246; Office 2A09) 

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[Chahat Upreti]

Hi Jim,

I am also working on C. elegans and would sincerely appreciate if the WS235 version of the genome was available in IGV. I have included a link to the FTP site which contains the genome and annotations here:

 

ftp://ftp.wormbase.org/pub/wormbase//releases/WS235/species/c_elegans

I was having difficulties trying to do this myself.

Regards,

Chahat

[James Robinson]

WS235 is added.  By default it only loads "Gene" annotations.  To load transcripts use "File > Load from server...".   If you want the full annotation set you will need to download the gff3 file,  then index it with either tabix (preferred) or igvtools.   After indexing use "File > Load from file..."

On Fri, Sep 22, 2017 at 11:30 AM, Chahat Upreti <chahatup...@gmail.com> wrote:

Hi Jim,

I am also working on C. elegans and would sincerely appreciate if the WS235 version of the genome was available in IGV. I have included a link to the FTP site which contains the genome and annotations here:

 

ftp://ftp.wormbase.org/pub/wormbase//releases/WS235/species/c_elegans

I was having difficulties trying to do this myself.

Regards,

Chahat

On Wednesday, February 24, 2016 at 5:30:17 PM UTC-6, Jim Robinson wrote:

Hi,

This is now available.  The annotation file had to be trimmed significantly, it's 3.5GB uncompressed.  I grepped out all the wormbase annotations, so what you'll see when you load it are those.  If you are interested in the entire file you will need to download it,  gunzip it, then index it with either tabix (best) or igvtools.  After doing this you can load it from the file menu.

On Wednesday, February 17, 2016 at 2:27:08 PM UTC-8, SM Pyonteck wrote:

Hi Jim,

I am also working on C. elegans and would sincerely appreciate if the WS245 version of the genome was available in IGV. I have included a link to the FTP site which contains the genome and annotations here:

ftp://ftp.sanger.ac.uk/pub/wormbase/FROZEN_RELEASES/WS245/species/c_elegans/PRJNA13758/

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