Where to Download & File Format of Reference Gene Annotation for C. elegans WS220(ce10)

Question

[smpyonteck]

Hello,

I would like to use the program BETA to integrate my RNA-seq differential expression data into the target gene calling for my ChIP-seq binding peaks (see: http://cistrome.org/BETA/tutorial.html#basic). BETA is not originally set up for the model organism C. elegans, so I need to prepare and input a reference gene annotation file using the following format:

Example

refseqID      chrom  strand  start     end       gname2
NM_032291     chr1   +       66999824  67210768  SGIP1
NM_001301823  chr1   +       33546729  33586132  AZIN2
NM_032785     chr1   -       48998526  50489626  AGBL4

I know that all of the information for the WS220(ce10) version of the C. elegans reference genome is available for download from the UCSC genome browser (http://hgdownload.soe.ucsc.edu/goldenPath/ce10/database/). However, there are multiple individual files available and I am unfamiliar with the formats and it is unclear to me which one I need. Is there anyone that has experience with this that can help? Thank you so much! I really appreciate it!

Answer 1

[Kirill Tsyganov]

Here is a link to WormBase ftp server ftp://ftp.wormbase.org/pub/wormbase/releases/WS220/species/c_elegans/

You should fine gff file there that will hold genome wide annotation.

You can also find any other information relating to C.elegans. I always thought that wormbase is the best place for anything related to worms.

Just one other thing WS220 is rather old version. I think current release WS247.

[smpyonteck]

Thank you! This was helpful for downloading the old version that I need (WS220).

Answer 2

[harold.smith.tarheel]

You can use WormMine from the WormBase site (available under 'Tools'). The query builder allows you to select the fields you need for the table shown in your example.

[smpyonteck]

Thank you! This is exactly what I needed. Much appreciated!

[smpyonteck]

Do you know if there is a way to modify the reference genome/annotation set to download from within WormMine? I was able to successfully pick the fields that I wanted to download, but it seemed that everything was from the WS238 version. I didn't see an obvious way to download information corresponding to a specific release, i.e. WS220. Thank you so much for your help!

Answer 3

[harold.smith.tarheel]

Apologies for the tardy reply; I didn't receive the alert for your follow-up question. For WS220, you can use the old WormMart tool (WormBase > Tools > More Tools). Choose Source 'WS220-bugFix', choose Database 'WS220-bugFix', choose Dataset 'Gene', choose Attributes 'Location > Genomic Position > Chr, Strand, Start, End', and choose 'Results.' Note that strand is represented by 1/-1, which you will need to convert to +/- after download.