User: dovi

gravatar for dovi
dovi30
Reputation:
30
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New User
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Last seen:
1 month ago
Joined:
2 years, 2 months ago
Email:
m***********@uni-hohenheim.de

Posts by dovi

<prev • 17 results • page 1 of 2 • next >
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TreeMix missing data?
... I just run [TreeMix][1] and I got weird results, I thought it might be because of missing data so I am wondering whether TreeMix handles missing data, and how it does it. The command line I used is: treemix -i input_file.gz -o out_treemix Missing data in my input_file.gz is given as `0,0` (ze ...
missing data treemix written 10 months ago by dovi30 • updated 8 months ago by Biostar ♦♦ 20
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VISTA annotation file
... Hi all, I am using VISTA (http://genome.lbl.gov/vista/index.shtml, in particular genomeVISTA tool) to align two genomes and browse the alignment. However I am not able to properly add the annotation file. I have added to the reference genome a gff file (as far as I know is a valid format for VISTA ...
annotation vista written 10 months ago by dovi30 • updated 8 months ago by lessismore480
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Comment: C: popoolation parallelization problem
... Well, I think my problem was related to the cluster I was using, sometimes jobs run as expected (talking about time) and sometimes they were 'delayed' and had to run them again (as they exceeded the 3 days time, that is the limit time in my cluster). I did the parallelisation as you say, I split t ...
written 10 months ago by dovi30
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Comment: C: popoolation parallelization problem
... It doesn't seem to generate a temporary file, for what I see in the code it directly prints the result into the output file ...
written 12 months ago by dovi30
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Comment: C: popoolation parallelization problem
... The cluster has the load manager MOAB, which schedules and manages all jobs, so I understand that if a job is running is because is not overloading the server and it can run properly (otherwise stays as 'waiting'). Or is not this what you mean? ...
written 12 months ago by dovi30
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popoolation parallelization problem
... Hi all, I am using [popoolation][1] for my pool-seq data to calculate fst values using `fst-sliding.pl` script. As the synchronized file weights ~2TB, I though that it would be better to parallelize the process. I've therefore split the synchronized file into small chunks and I run multiple jobs ( ...
cluster popoolation parallelize written 12 months ago by dovi30
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Answer: A: cnv-seq reference hit
... So far my solution was to create a "dummy" reference sample hit that contains all positions as they also do in CNVkit when no "normal" sample is provided. ...
written 12 months ago by dovi30
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Comment: C: Cnvnator Output File
... If you are using a server you need to ssh with `ssh -X`, otherwise you can't see the plot. ...
written 12 months ago by dovi30
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cnv-seq reference hit
... Hi all, I've read that CNV-seq needs a reference hit file. Is this reference file the actual reference genome (the one I used to map my reads)? Or I have to pick up one of my samples to be a reference hit file ? (I don't have "treatment/control" samples). In the case that should be the actual refe ...
cnv-seq readdepth cnv written 12 months ago by dovi30
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Comment: C: bamCompare log2 ratio p-value
... Thanks for the reply, I guess I'll try another approach than bamCompare. ...
written 12 months ago by dovi30

Latest awards to dovi

Supporter 4 months ago, voted at least 25 times.
Scholar 12 months ago, created an answer that has been accepted. For A: blastx generates empty output file
Scholar 12 months ago, created an answer that has been accepted. For A: blastx generates empty output file

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