User: gandrescabrera

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Posts by gandrescabrera

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Comment: A: what is the difference between GRCh37 and hg19 ?
... Can I make a similar answer in here? Might be useful to others too. If its innapropiate take the according action to fix it, sorry. Which is the difference between Homo_sapiens.GRCh38.91 and Homo_sapiens.GRCh38.78? Can I use a Homo_sapiens.GRCh38.91.bed as annotation to a genome referenced to Homo_ ...
written 16 months ago by gandrescabrera80
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Comment: C: Recommended Tools For 3'UTR APA Detection From Rna-Seq Data?
... Hey I had found this tool called "APATrap" which seems to work pretty good, and has comparations with DaParse and ChangePoint. The package "roar" was good for a first impression, but its still under development, I guess it gave me little information about the most expressed APAs, but little informat ...
written 17 months ago by gandrescabrera80
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Comment: C: Recommended Tools For 3'UTR APA Detection From Rna-Seq Data?
... Hello, and thanks for your recommendation. Btw, what did you mean with "cf"? Lets stay in touch, i'm glad to collaborate. ...
written 24 months ago by gandrescabrera80
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Answer: A: Ideas about what can I do with the raw data of gene expression and miRNA of Gene
... I will ask you some items: RNAseq data? Tissue specific? Genome version (hg19/hg38?) Bibliography about drugs you used? I think if you have RNAseq data that you could check about alternative splicing events on drug use. For that you can use a featureCounts (R package) for mapping the alignments ...
written 24 months ago by gandrescabrera80
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Recommended Tools For 3'UTR APA Detection From Rna-Seq Data?
... {tl;dr}looking for useful tools for 3'UTR dynamic expression detection at transcriptomic data Hi, I have been working with RNAseq data, looking for different events like alternative splicing. Now I have a question about the 3'UTR shortening/lengthening between 2 conditions on humans. I have be ...
R tools utr rna-seq polyadenylation written 24 months ago by gandrescabrera80 • updated 24 months ago by i.sudbery5.2k
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Comment: C: GTF File contains multiple gene ids for the same gene name?
... You were lucky, I found the source: "We recommend to use unique gene identifiers, such as NCBI Entrez gene identifiers, to cluster features into meta-features. **Gene names are not recommended to use for this purpose because different genes may have the same names.** Unique gene identifiers were of ...
written 2.1 years ago by gandrescabrera80
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Answer: A: GTF File contains multiple gene ids for the same gene name?
... I recommend you to use Ensembl or Havana ID's instead of Gene Names, because Gene Names aren't in a consensus, as Ensembl/Havana/Gencode did in the past which their ID's. I had'nt checked it out, but I read it on the web and I have been told in my job to use ENS Id's. You could then give the ID's t ...
written 2.1 years ago by gandrescabrera80
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Answer: A: How to create 'gene' and 'transcript' entries in a GTF containing only exons
... I dont know if you are looking for a R based solution, but since I saw you were using R studio I will give it a shot. 1) Download from Biomart a .gz file with "Exon ID", "Transcript ID", and "Gene ID" 2) Read it on R with the read.delim() function, or read.csv() function 3) Use merge() function to ...
written 2.1 years ago by gandrescabrera80
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Answer: C: Finding appropriate bioinformatic problem sets for a beginner (R, Python)
... I would recommend you some manuals from R packages. You will find a lot in Bioconductor. For example edgeR have real-world examples as case examples, which you can DL the datasets. https://bioconductor.org/packages/release/bioc/vignettes/edgeR/inst/doc/edgeRUsersGuide.pdf This is nice because is b ...
written 2.2 years ago by gandrescabrera80
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Comment: C: Finding appropriate bioinformatic problem sets for a beginner (R, Python)
... Nice recomendation! ...
written 2.2 years ago by gandrescabrera80

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