User: Sergio Martínez Cuesta

Reputation:
60
Status:
Trusted
Location:
Cambridge, UK
Website:
https://github.com/semacu
Scholar ID:
Google Scholar Page
Last seen:
2 days, 19 hours ago
Joined:
1 year, 8 months ago
Email:
s********@gmail.com

Posts by Sergio Martínez Cuesta

<prev • 12 results • page 1 of 2 • next >
0
votes
0
answers
61
views
0
answers
Convert regions from genomic coordinates to transcript coordinates
... This is an attempt to convert a bed file containing regions of interest from genomic coordinates to transcript coordinates. If you have come across something related or know a better way of doing this, it would be great to know. The regions of interest and transcripts in genomic coordinates: h ...
genome bed transcript written 13 days ago by Sergio Martínez Cuesta60
2
votes
1
answer
308
views
1
answer
Transcript biotypes for ncRNA in GRCh37 using biomaRt?
... Dear all, I am attempting to retrieve transcript biotypes for ncRNAs using Bioconductors's biomaRt in GRCh37 as follows: library(biomaRt) ensembl <- useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", dataset="hsapiens_gene_ensembl") # biotypes for mRNAs are obtaine ...
grch37 biomart biotype transcripts ncrna written 6 months ago by Sergio Martínez Cuesta60 • updated 6 months ago by Emily_Ensembl17k
0
votes
0
answers
211
views
0
answers
Transcript features and annotations
... I am planning a trancriptome alignment of iCLIP sequencing data. How can I link UCSC hg19 transcript ids with transcript features e.g. coding, non-coding, lncRNA, antisense, pseudogene ...? I downloaded [iGenome's UCSC hg19 reference genome][1] and used the genes.gtf file available with the downloa ...
alignment transcript written 7 months ago by Sergio Martínez Cuesta60 • updated 7 months ago by Biostar ♦♦ 20
5
votes
1
answer
574
views
5 follow
1
answer
Obtaining hg38 gene features: promoters, 5'UTR, exons, introns, 3'UTR
... Which approach do you find useful to extract gene features (promoters, 5'UTR, exons, introns, 3'UTR ) from the annotation file (genes.gtf) of a reference genome e.g. the [iGenomes UCSC hg38][1]? I often use the functions available in the [GenomicFeatures bioconductor package][2], e.g. makeTxDbFromG ...
gene hg38 genomic features written 8 months ago by Sergio Martínez Cuesta60 • updated 8 months ago by ATpoint13k
0
votes
2
answers
396
views
2
answers
Comment: C: Ideas to split peaks into subpeaks - beyond PeakSplitter
... Good point, we do not know if they are meaningful / noise. These are ChIP-seq datasets. I think it comes down to the issue of finding narrower peaks to the ones found so far with existing arguments. Perhaps tweaking arguments in the peak callers would give me the finer detail I am looking for. ...
written 9 months ago by Sergio Martínez Cuesta60
5
votes
2
answers
396
views
5 follow
2
answers
Ideas to split peaks into subpeaks - beyond PeakSplitter
... Here are some thoughts regarding how to break down bed files into smaller (perhaps more concrete) bed files using signal / read counts from e.g. wig or bedgraph files. One possible scenario would be: you have identified peaks (treatment vs. control) using callers such as macs2, however after having ...
peak calling wig chip-seq written 9 months ago by Sergio Martínez Cuesta60 • updated 10 weeks ago by Biostar ♦♦ 20
0
votes
1
answer
603
views
1
answers
Comment: C: Associations between biological terms and gene names in the literature
... Thanks Maria, Can you elaborate on how to derive a score for strength of association between text mined annotations obtained using Europe PMC API, please? ...
written 12 months ago by Sergio Martínez Cuesta60
0
votes
0
answers
461
views
0
answers
News: Final Week for Early Bird Prices: Engaging Researchers in Good Data Management - 15th November, Cambridge
... Dear all, The following one-day conference may be of interest to some of you. Early bird registration closes in one week! All the best, Sergio ---------------------------------------------------- **Engaging Researchers in Good Data Management** A one-day conference 15 November 2017, St Catha ...
2
votes
0
answers
448
views
0
answers
News: Registrations open: Engaging Researchers in Good Data Management - 15th November 2017, Cambridge, UK
... Dear all, Registrations are now open for this **one-day conference** taking place in **Cambridge, UK** on the **15th November 2017**. It may be relevant to those interested in learning more and discussing *data sharing and management* in life sciences and other research disciplines. Please find mo ...
data news conference research life sciences written 17 months ago by Sergio Martínez Cuesta60 • updated 17 months ago by genomax62k
1
vote
1
answer
603
views
1
answer
Associations between biological terms and gene names in the literature
... Dear all, Given a biological term(s) of interest (e.g. G-quadruplex: MeSH Unique ID: [D054856][1]), I am looking for a robust tool to extract all known human gene names (e.g. TP53, P53) found to co-occur in proximity to my query biological term in the entire body of abstracts / freely available mai ...
literature text mining pubmed written 18 months ago by Sergio Martínez Cuesta60 • updated 12 months ago by Maria_Levchenko60

Latest awards to Sergio Martínez Cuesta

Popular Question 6 months ago, created a question with more than 1,000 views. For RNA-seq HEK293T recent datasets

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1830 users visited in the last hour