User: thefirstrealace

Reputation:
30
Status:
New User
Location:
Germany
Last seen:
2 years, 6 months ago
Joined:
3 years, 4 months ago
Email:
t**************@gmail.com

Posts by thefirstrealace

<prev • 29 results • page 1 of 3 • next >
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Genestack: Download results
... Hello everybody, i just finished a WGBS analysis with the proposed standard pipeline on genestack and i would like to download/export the methylation ratio results file, but can't seem to find any way to do that ... at least not on their homepage. I googled for a while now and all i found out is, t ...
genestack written 2.6 years ago by thefirstrealace30
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Scatter plot: Multi-dimensional property A against one-dimensioal property B
... Hello everbody, i need to find a possible correlation between a multidimensional porperty A and a one dimensional property B. In particular, i have the following properties: - Property A: Sequence of ~10 to ~15 binned methylation ratios within an exon - Property B: Length of the exon My data se ...
R scatter plot written 2.6 years ago by thefirstrealace30
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Comment: C: Local Galaxy: Need help with HISAT index builder
... Hi, your method worked perfectly fine. I could directly use the downloaded ht2 indexes from the hisat homepage after changing the .loc file and restarting my local galaxy. Thanks alot for the help. ...
written 2.6 years ago by thefirstrealace30
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Local Galaxy: Need help with HISAT index builder
... Hello everybody, i recently installed a local galaxy version and added some tools via toolshed including HISAT. I attempted to build an index for hg19 with the HISAT index builder, but it wont work at all. This is what i have done so far: 1. Install HISAT (+ all dependencies automatically) 2. In ...
local galaxy hisat index builder written 2.6 years ago by thefirstrealace30 • updated 2.6 years ago by Devon Ryan88k
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Comment: C: DNA methylation (wig format): Is a quantile normalization across multiple sample
... Im glad to hear that i do not have to perform a normalization across my samples, since such a procedure also may lead to a loss of potentially interesting features (from a purely biological point of view). Thanks again for your help. ...
written 2.7 years ago by thefirstrealace30
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DNA methylation (wig format): Is a quantile normalization across multiple samples neccesary?
... Hello everyone, i have the following problem. I am currently comparing the methylation profile around certain genomic regions. I have downloaded methylomes of three different human tissues/cell types from the GEO database. These methylaomes are all in bed format and look like shown below: ------- ...
dna methylation wig normalization written 2.7 years ago by thefirstrealace30
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Comment: C: Calculate binned methylation data throughout hg19 with BEDOPS
... Hi, thank you very much for your reply. However, my methylation file is in bed format. Is it possible to use my methylation.bed as input parameter? best regards ...
written 2.7 years ago by thefirstrealace30
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Comment: C: Digitize methylation data throughout hg19
... Im not too sure about that myself to be honest. Some sources say that it should be the mean of all values within a bin and some say, that it should be the number of methylated CpG divided by the number of all CpG within a bin. Apparently the "one and only correct way" does not exist. ...
written 3.0 years ago by thefirstrealace30
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Comment: C: Digitize methylation data throughout hg19
... Hi, it is true, that the terms are actually misleading. What i meant is, that i need to convert the existing 1 bp resolution methylation data that i have downloaded into 20 bp resolution data. The downloaded methylation file (1 bp resolution) stores for each cytosine the methylation value between ...
written 3.0 years ago by thefirstrealace30
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Need help with Mann-Whitney-U Test
... Hello, i have the following problem: In a practical course, i have obtained a quite big data set X of measurements and slightly smaller data sets Y1 and Y2. I need to use the Mann-Whitney-U test in order to find out, if the measurements Y1 and Y2 are either significantly smaller or significantly bi ...
mann-whitney-u statistical test written 3.1 years ago by thefirstrealace30 • updated 3.1 years ago by reilly.brian.m50

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Scholar 3.4 years ago, created an answer that has been accepted. For A: Ubuntu: MISO unittest fails

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