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-   -   Help with GenomicFeatures package from Bioconductor (http://seqanswers.com/forums/showthread.php?t=49489)

diego diaz 01-12-2015 01:05 PM

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!!

dpryan 01-12-2015 01:47 PM

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().

diego diaz 01-14-2015 07:53 AM

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.


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