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!
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smpyonteck •
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.
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Kirill Tsyganov
Thank you! This was helpful for downloading the old version that I need (WS220).
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smpyonteck •
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.
Thank you! This is exactly what I needed. Much appreciated!
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!
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smpyonteck •
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.
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harold.smith.tarheel
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