User: Sergio Martínez Cuesta

Reputation:
50
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Trusted
Location:
Cambridge, UK
Website:
https://github.com/semacu
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Google Scholar Page
Last seen:
2 days, 15 hours ago
Joined:
1 year, 1 month ago
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Posts by Sergio Martínez Cuesta

<prev • 10 results • page 1 of 1 • next >
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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 8 days ago by Sergio Martínez Cuesta50 • updated 2 days ago by Biostar ♦♦ 20
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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 5 weeks ago by Sergio Martínez Cuesta50 • updated 5 weeks ago by ATpoint5.7k
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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 weeks ago by Sergio Martínez Cuesta50
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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 weeks ago by Sergio Martínez Cuesta50 • updated 9 weeks ago by Rashedul Islam220
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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 5 months ago by Sergio Martínez Cuesta50
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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 ...
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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 9 months ago by Sergio Martínez Cuesta50 • updated 9 months ago by genomax52k
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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 11 months ago by Sergio Martínez Cuesta50 • updated 5 months ago by Maria_Levchenko40
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RNA-seq HEK293T recent datasets
... Dear all, I am currently exploring ArrayExpress/GEO for relevant datasets, but I was wondering if anyone is aware/have used any recent RNA-seq datasets involving the human cell line HEK293T? The classical datasets are from 2008 and 2010: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11892 ...
hek293t rna-seq written 12 months ago by Sergio Martínez Cuesta50 • updated 11 months ago by vivekbhr500
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HeLa reference fasta
... Dear all, My first question is if there is / where to find a referece .fasta file for the HeLa cell line. I am working with several DNA sequencing samples from HeLa. So far I have used UCSC's hg19 as a reference, however when aligning with bwa I can see a lot of R1 fwd alignments with a lot of so ...
reference hela hg19 written 13 months ago by Sergio Martínez Cuesta50

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