User: R.Blues

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R.Blues80
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3 months, 1 week ago
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4 years, 5 months ago
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Posts by R.Blues

<prev • 44 results • page 1 of 5 • next >
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Answer: A: Reading Clariom D Human CEL files results in missing CDF enviroment error
... Mmmmm. Have you tried taking a look at their CustomCDF package? Maybe there is something on it that you can use http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp#v22 Please let us know if that worked! :) ...
written 3 months ago by R.Blues80
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Hi-C, inferring contacts from normalized matrixes
... Hello everyone, I am sorry for bothering you, but I would like to know if there is a simple way to infer, from Hi-C data, which bins are in contact with others, just using directly the normalized matrixes. In my case I am trying to do this with the 40kb bin size datasets of Ren Lab (http://chromos ...
hi-c chromatine written 14 months ago by R.Blues80
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Obtain all ncDNA sequences using a GTF
... Hi everyone. I am asking something that may seem trivial, but I would like to know how others would do it. I need to work with all the non-coding DNA sequences of *M. musculus*, so my first crucial step is retrieving these sequences. Let's say I am using the Ensembl GTFs of their most recent g ...
genome sequence written 19 months ago by R.Blues80
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Alternative splicing database - Pathogenies
... Hello everyone, I am trying to check if a homemade alternative splicing (in human cells) also happens in some pathogenies (specially regarding cancer). I have searched the DBASS database, and I am trying to check the SpliceDisease and H-DBAS, although their server is down, and they probably quite o ...
pathogenies database splicing written 23 months ago by R.Blues80
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Comment: C: How to identify TSS sites from bacterial RNA-Seq data?
... I'll give it a try and let you know. Thank you very much!! ...
written 2.0 years ago by R.Blues80
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Comment: C: How to identify TSS sites from bacterial RNA-Seq data?
... Yes, I know, but I do not have 5-prime enriched data. ...
written 2.0 years ago by R.Blues80
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Comment: C: How to identify TSS sites from bacterial RNA-Seq data?
... No, I haven't! I didn't know it can be used for TSS discovery. Would you mind telling me how? I do not find any TSS mention in the manual. ...
written 2.0 years ago by R.Blues80
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Variant Effect Predictor parameters for custom gff and fasta
... Hello everyone, I am learning to use Ensemble VEP (Variant Effect Predictor) in command line mode. I am interested in predicting the effect of variants in an not-standard genome, with my own annotation. I am using the VEP Github pre-release version (it is a new version, https://github.com/Ensembl/ ...
fasta gff vep snp written 2.0 years ago by R.Blues80 • updated 7 months ago by nicolas.dussex30
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Comment: C: Pseudoautosomal regions (PAR) coordinates in different species, where and how?
... Wow, it is really nice. At least I know that I cannot expect to know the PAR in rat! However, there are no coordinates or supplementary material in the paper. Do you know where could I find this information? Thank you very much for your help. ...
written 2.1 years ago by R.Blues80
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Pseudoautosomal regions (PAR) coordinates in different species, where and how?
... Hello all, I am trying to find the coordinates of pseudoautosomal regions (PAR) in different species, such as human, mouse and rat. So far I have just found the coordinates for human, in hg19, via http://genome.ucsc.edu/cgi-bin/hgGateway. But... how can I find the coordinates for other species suc ...
genome sequence written 2.1 years ago by R.Blues80 • updated 22 months ago by Santosh Anand4.4k

Latest awards to R.Blues

Popular Question 14 months ago, created a question with more than 1,000 views. For Three microarray questions: Oligo package, custom microarrays and makeContrasts
Popular Question 14 months ago, created a question with more than 1,000 views. For cn.mops for WES, what am I doing wrong?
Popular Question 14 months ago, created a question with more than 1,000 views. For Python and SNP Databases, how?
Popular Question 14 months ago, created a question with more than 1,000 views. For How to identify TSS sites from bacterial RNA-Seq data?
Popular Question 14 months ago, created a question with more than 1,000 views. For Pseudoautosomal regions (PAR) coordinates in different species, where and how?
Supporter 2.2 years ago, voted at least 25 times.
Popular Question 2.5 years ago, created a question with more than 1,000 views. For cn.mops for WES, what am I doing wrong?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For cn.mops for WES, what am I doing wrong?
Popular Question 4.1 years ago, created a question with more than 1,000 views. For How to correlate genes to transcription factors in RNA-Seq data?

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