SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bioconductor package GeneR buthercup_ch Bioinformatics 0 10-20-2014 02:24 AM
Bioconductor package -GADEM DNASpeaks Complete Genomics 1 06-04-2013 06:52 AM
Problem with Bioconductor ArrayExpressHTS package ilya.kuzovkin Bioinformatics 1 01-18-2013 08:13 AM
a question about the use of R package-GenomicFeatures masylichu Bioinformatics 5 12-08-2010 05:26 PM

Reply
 
Thread Tools
Old 01-12-2015, 12:05 PM   #1
diego diaz
Member
 
Location: Santiago, Chile

Join Date: Oct 2013
Posts: 62
Default Help with GenomicFeatures package from Bioconductor

Hi all

I am new using GenomicFeatures package from Bioconductor and I am a little stuck. I need to get tRNA annotations, but I don't see the tRNA table in the function supportedUCSCtables(). However, if I check the UCSC site, tRNA table is available.

Also I tried to get miRNAs annotations. but I couldn't

All is for Mus musculus (mm10)

Thanks in advance!!

Last edited by diego diaz; 01-14-2015 at 07:00 AM.
diego diaz is offline   Reply With Quote
Old 01-12-2015, 12:47 PM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,479
Default

The tables are actually hard-coded, see here (N.B., that's an old version, but that part of the code hasn't changed substantially). You can always download the table from UCSC (or biomart if you prefer the Ensembl annotation, which you should) and then use makeTranscriptDbFromGff().
dpryan is offline   Reply With Quote
Old 01-14-2015, 06:53 AM   #3
diego diaz
Member
 
Location: Santiago, Chile

Join Date: Oct 2013
Posts: 62
Default

Thanks for your repply.

I decided to use biomaRt to get the ncRNA annotations from Ensembl. I think it is more "friendly" than GFeatures. tRNA annotations weren't available in biomart (or I didn't know how to get it), thus I chose download them from UCSC site.

In any case, I put the code that I used if it is useful for someone:

library(biomart)
ensembl=useMart("ensembl")
ensembl = useDataset("mmusculus_gene_ensembl",mart=ensembl)
filters=c("transcript_biotype")
attr=c("chromosome_name","start_position","end_position","external_gene_name","strand","transcript_biotype")
values=c("lincRNA","miRNA","misc_RNA","Mt_rRNA","Mt_tRNA","rRNA","snoRNA","snRNA")
ncRNA.annot <- getBM(attr,filters=filters,values=values,ensembl)
ncRNA.annot$chromosome_name <- paste0("chr",ncRNA.annot$chromosome_name)
ncRNA.ranges <-with(ncRNA.annot,GRanges(chromosome_name,IRanges(start_position,end_position,names=external_gene_name),strand=strand, transcript_type=transcript_biotype))


Thanks again.

PD: the idea of use biomaRt or GenomicFeatures was to try automate the analysis. But I think bam files and tRNA annotation as inputs in my script is acceptable.

Last edited by diego diaz; 01-14-2015 at 07:01 AM.
diego diaz is offline   Reply With Quote
Reply

Tags
annotation, bioconductor, genomicfeatures

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:28 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO