User: Cumol

gravatar for Cumol
Cumol40
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40
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11 months, 1 week ago
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3 years, 1 month ago
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m************@gmail.com

Posts by Cumol

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Align RNA-seq data to a custom list of exons?
... How do I turn my exon sequences into the fasta format? The only idea I had was to blast them against the target genome (using ensembl) and then convert the output into GTF. But it doesn't seem to be so straight forward. Is there a better option? ...
written 11 months ago by Cumol40
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Comment: C: Align RNA-seq data to a custom list of exons?
... What is the best way to edit the GTF file? Would I remove the lines associated with the Gene I am interested in and then add my custom lines? I will probably need the exact start and end of each exon on the genome I am using for indexing, right? ...
written 11 months ago by Cumol40
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Align RNA-seq data to a custom list of exons?
... A recent publication investigated splice variants of a gene I am interested in (using SMRT seq) and they described different/additional exons compared to what I find in NCBI or ENSEMBL. I wanted to analyze splice variants and exon counts of this gene using the described exons from this publication ...
alignment rna-seq exon written 11 months ago by Cumol40
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Answer: A: Where can I find public Singel Cell RNAseq data?
... Here you will find one: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE59739 It is from this publication: Usoskin, D. et al. Unbiased classification of sensory neuron types by large-scale single-cell RNA sequencing. Nat Neurosci 18, 145–153 (2015). ...
written 3.1 years ago by Cumol40
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Comment: C: Ensembl datacentre shut-down: Friday 26th August - Tuesday 30th August 2016
... Does not seem to work for me using this: > library(biomaRt) >listMarts(host = "asiadb.ensembl.org", port = 5306) I get the error: >Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check ...
written 3.1 years ago by Cumol40

Latest awards to Cumol

Scholar 3.1 years ago, created an answer that has been accepted. For A: Where can I find public Singel Cell RNAseq data?

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