User: alhafidzhamdan

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Posts by alhafidzhamdan

<prev • 14 results • page 1 of 2 • next >
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Comment: C: unable to access executable in PATH from remote server
... Thanks a lot for this! very helpful and easiest to do. ...
written 11 weeks ago by alhafidzhamdan0
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Comment: C: How to increase RAM for R scripts run in computer cluster
... Essentially this -> https://github.com/mskcc/facets/blob/master/inst/extRfns/readSnpMatrixDT.R ...
written 3 months ago by alhafidzhamdan0
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Comment: C: How to increase RAM for R scripts run in computer cluster
... That's for windows- i'm using linux ie computer cluster. ...
written 3 months ago by alhafidzhamdan0
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How to increase RAM for R scripts run in computer cluster
... Hi all, This is probably not specific to facets but i am struggling to run facets.R in an HPC (linux). My command: > Rscript --vanilla facets.R > -i $PATIENT_ID > -f $INPUT > -o $OUTPUT > -c $CVAL > > Loading required package: pctGCdata > Taki ...
cluster R ram linux written 3 months ago by alhafidzhamdan0
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How to download data stored in git lfs
... Hi all, I am trying to download thsi RData file from a repository > https://raw.githubusercontent.com/lawrenson-lab/Non-coding-Somatic-Mutations-in-OvCa/master/RData/diffBind_session03_step02.RData However the file is stored in git lfs system and i am not sure how to download it? > versio ...
git lfs written 4 months ago by alhafidzhamdan0
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Comment: C: Error in GATK GenomicsDBImport
... Just remove the directory "db_177" and try again. But make sure genomics_DBs directory has been created. ...
written 4 months ago by alhafidzhamdan0
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Comment: A: blast error ?creating index
... Thanks guys! It turned out i didn't have the .nal files as memory had run out. So I re-ran it with enough memory and it worked fine. ...
written 5 months ago by alhafidzhamdan0
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Saturation analysis of chip-seq peaks
... Dear all, I have broad peak files generated by MACS2 for 68 samples. I want to see if I have reached saturation of new peaks obtained in my samples. I want to produce a graph similar to the one here -> https://ibb.co/Lnx64xG My question is does anyone know how to generate this? Is there an R pac ...
R chip-seq written 5 months ago by alhafidzhamdan0
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Comment: C: blast error ?creating index
... Sorry that was my bad- there wasn't any space in the actual run. ...
written 5 months ago by alhafidzhamdan0
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Comment: C: blast error ?creating index
... It is 177G . And there is no .nal file. just lots of .nhr .nin .nsq and no .nog .nsd .nsi (as for hg38 when i tested this). ...
written 5 months ago by alhafidzhamdan0

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