User: R.Blues

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R.Blues60
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Posts by R.Blues

<prev • 43 results • page 1 of 5 • next >
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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 11 weeks ago by R.Blues60
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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 7 months ago by R.Blues60
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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 11 months ago by R.Blues60
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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 12 months ago by R.Blues60
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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 12 months ago by R.Blues60
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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 12 months ago by R.Blues60
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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 12 months ago by R.Blues60
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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 13 months ago by R.Blues60
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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 13 months ago by R.Blues60 • updated 10 months ago by Santosh Anand3.2k
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How to identify TSS sites from bacterial RNA-Seq data?
... Hello all, I know this has been asked a lot, but I am trying to predict TSS sites with bacterial RNA-Seq data (I have a reference genome and annotation). It is standard paired-end RNA-Seq data, not enriched or dRNA-Seq. I know it can be done, but... I cannot find how. Which programme, R package, e ...
rna-seq tss written 13 months ago by R.Blues60 • updated 12 months ago by Charles Plessy2.4k

Latest awards to R.Blues

Supporter 14 months ago, voted at least 25 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For cn.mops for WES, what am I doing wrong?
Popular Question 22 months ago, created a question with more than 1,000 views. For cn.mops for WES, what am I doing wrong?
Popular Question 3.1 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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