User: ResearchR

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ResearchR40
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5 days, 4 hours ago
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1 year, 8 months ago
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Posts by ResearchR

<prev • 25 results • page 1 of 3 • next >
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(Closed) Building Compute Cluster
... Dear Bioinformaticians, I hope this question is correctly placed here and hope that you have a few suggestions for me. A colleague and me would like to build our own computer cluster, but since we do not have funding to hire someone to do so, we have to do this by ourself. 1. Do you have any bo ...
high performance computing compute cluster written 11 days ago by ResearchR40
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Answer: A: Best tool for Motif enrichment of TFs
... Maybe this helps:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702883/ ...
written 3 months ago by ResearchR40
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Comment: C: Long Reads: Nanopore/ PacBio
... >Using small reads, like Illumina provides, 400X are needed for whole exome to detect SNV or CNV Sorry, I am a bit caught up in some of our recent samples, where we used such deep exome sequencing due to very rare combination genetic disorders and this is the only exome seq I work with so far (I ...
written 3 months ago by ResearchR40
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Comment: C: Long Reads: Nanopore/ PacBio
... Thanks for the fast reply. The second publication I read before, and this is what keeps me wondering. On the Nanopore webpage, they claim that the flow-cell of the PromethION can theoretically read max 350GB, but in practice 150GB are reached. When reading publications using this device, something ...
written 3 months ago by ResearchR40
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Long Reads: Nanopore/ PacBio
... Hi all, I would like to know more about long read sequencing like Nanopore or PacBio does. Getting the basic biochemistry behind the idea and the current problems (higher error rate i.e due to homopolymers) was not a big issue, but processing and making actual use of the data (in a bioinformatica ...
indel nanopre cnv snv longreads written 3 months ago by ResearchR40
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Answer: A: Gene Paralogs from GeneCards or Genes Like Me
... Web crawling does not seem to work that nicely. Found the following suggestion: https://support.bioconductor.org/p/105070/ ...
written 3 months ago by ResearchR40
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Defining Gene Paralogs
... Hi guys, I am looking for a data base, which reports paralogs for (human) genes, for instance like *GeneCards* does. I already wrote a webpage crawler to access this information, but it takes way too long for the amount of genes I have. Data bases like [Duplicated Genes DB][1] or Ensemble provide s ...
gene rna-seq written 3 months ago by ResearchR40
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Distinguish Single Cell DNA Sequencing: Human vs Mouse
... Hey guys, I have a quick question - When doing single cell DNA sequencing from human mouse xenograft models - how to confirm via bioinformatic way that the sequence alignment obtained, is from human cell and not mouse cell contamination. Do you think it is enough to look at sequence alignment st ...
single cell sequencing sequencing written 5 months ago by ResearchR40 • updated 5 months ago by h.mon23k
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Genomic Annotation of Y_RNA
... Dear all, does anyone of you know a comprehensive annotation of Y_RNA (Gencode does not include them and NCBI annotation seems to miss one)? Best, Chris P.S.: I am using Gencode for everything else (normally) ...
genome mirna rna-seq sequencing written 5 months ago by ResearchR40
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Comment: C: CpG Density with respect to TSS
... Thanks for the suggestion! I will give it a try! ...
written 7 months ago by ResearchR40

Latest awards to ResearchR

Popular Question 3 months ago, created a question with more than 1,000 views. For Predicting binding probability of circRNA and miRNA
Scholar 3 months ago, created an answer that has been accepted. For A: Gene Paralogs from GeneCards or Genes Like Me
Popular Question 5 months ago, created a question with more than 1,000 views. For Coordinates for Transcription Start Site (TSS)

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