User: dovi

gravatar for dovi
dovi30
Reputation:
30
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New User
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Last seen:
1 week, 4 days ago
Joined:
1 year, 8 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 3 months ago by dovi30 • updated 8 weeks 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 4 months ago by dovi30 • updated 10 weeks ago by lessismore370
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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 4 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 6 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 6 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 6 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 6 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 6 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 6 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 6 months ago by dovi30

Latest awards to dovi

Scholar 6 months ago, created an answer that has been accepted. For A: blastx generates empty output file
Scholar 6 months ago, created an answer that has been accepted. For A: blastx generates empty output file

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