User: Sergio Martínez Cuesta

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60
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Location:
Cambridge, UK
Website:
https://github.com/semacu
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1 month, 3 weeks ago
Joined:
2 years, 1 month ago
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Posts by Sergio Martínez Cuesta

<prev • 16 results • page 1 of 2 • next >
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Fixing atom valences
... Dear all, Does anyone know how to fix atom valences (nitrogens in the example below) that are greater than permitted by tools like RDKit? The input is a smiles strings or a mol file. E.g. here is the smiles string for the invalid molecule depicted underneath: CN1=C(C=CC=C1)c2c3C=Cc(n3)c(C4=CC=CC= ...
smiles cheminformatics written 3 months ago by Sergio Martínez Cuesta60
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Comment: C: Weighted sequence logos and motifs
... Thank you, I had a read through the docs. Even though you can input what they call seeds, I could not find a way to incorporate sequence scores into the motif discovery. ...
written 3 months ago by Sergio Martínez Cuesta60
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Comment: C: Weighted sequence logos and motifs
... That could work! But when adding sequences I would have to round decimal numbers to integers, which could result in a huge number of sequences after all, however this may not be a problem here. ...
written 3 months ago by Sergio Martínez Cuesta60
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Weighted sequence logos and motifs
... Dear all, Most libraries and software aimed at obtaining DNA sequence logos (e.g. ggseqlogo) or discovering sequence motifs (e.g. MEME tools) take as an input a fasta file containing a list of sequences: >seq1 AGATCATCATCTCAT >seq2 GTCTAGCTACGTACT >seq3 TGCATGCATGC ...
motif logo written 3 months ago by Sergio Martínez Cuesta60
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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 5 months ago by Sergio Martínez Cuesta60
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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 11 months ago by Sergio Martínez Cuesta60 • updated 11 months ago by Emily_Ensembl18k
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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 12 months ago by Sergio Martínez Cuesta60 • updated 12 months 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 13 months ago by Sergio Martínez Cuesta60 • updated 13 months ago by ATpoint19k
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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 14 months ago by Sergio Martínez Cuesta60
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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 14 months ago by Sergio Martínez Cuesta60 • updated 7 months ago by Biostar ♦♦ 20

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Popular Question 11 months ago, created a question with more than 1,000 views. For RNA-seq HEK293T recent datasets

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