Is there a way to use bioMART on the ensemble.org website to retrieve genomic sequences in a window (ie. 500 bp) both upstream and downstream of the annotated TSS for selected genes? So far, I can only retrieve genomic sequences either upstream or downstream, but not both.
•
written
by
daniel.zhang •
2 answers
Do you really need biomart?
If not you can download gff with gene information, extract only genes to bed with TSS coordinate for both start and end (2nd and 3rd columns) with awk and use samtools slop to retrieve requested range. Retrieval of TSS to bed should be done for each strand separately.
As you see it requires some coding. Maybe somebody else can provide simpler solution.
You could use the Ensembl REST API. Use one of the Lookup endpoints to get the TSS of the gene (check the strand, if the gene is +, TSS is the start, if it's -, TSS is the end). Then use that with the sequence region endpoint to get that sequence with the expand options. You can copy most of the code from exercise 5.2 of this online course but just switch to the sequence endpoint.
Log in to answer this question.
-
ChIPseeker annotation
written by sk_24 •
-
deeptools computeMatrix reference-point, want to plot 1kb before TSS and 1kb after TES then use plo…
written by jennxyzhang •
-
Annotating narrow.peak to promoter region using GenomicFeatures
written by solaris •
-
Can getSequence get sequence of coding and its upstream in one entry?
written by oboeconcerto314 •
-
Extracting Flanking Regions across TSS using R scripts
written by r.tor •
-
Retrieve promoter sequences of all human genes
written by JJ
-
overlapping genes in lncrna prediction
written by dineshtripathy9658 •
-
How to get downstream promoter sequences using BiomaRt
written by FLDal •
-
Annotate Regions In Bed File With Nearest Downstream Gene
written by jxchong
-
How To Identify/Flag The Presence Of Indels On The Read Level Nearby A Given Position In A Bam File?
written by Anders Bergström •
