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User: vakul.mohanty

gravatar for vakul.mohanty
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Location:
United States
Last seen:
1 year, 7 months ago
Joined:
3 years, 8 months ago
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v************@gmail.com

Posts by vakul.mohanty

<prev • 24 results • page 1 of 3 • next >
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qCount with a GRangesList is very slow
... Hello, I'm using QuasR package to process some RNAseq I have and count reads in exonic and intronic regions of all genes in the human genome. To this end I have aligned the reads and use qCount to carry out my counting using a GrangesList as the query. The list an entry for each gene and the entry ...
quasr grangeslist qcount written 19 months ago by vakul.mohanty10
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Comment: C: Running DEXSeq in a distributed setting
... Hi, Alejandro, Thanx! I'll look into the vignette and give it a shot.  Thank you for the pointer!  Vakul  ...
written 21 months ago by vakul.mohanty10
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Running DEXSeq in a distributed setting
... Hello,  I have a cohort of ~500 human RNAseq samples that I want to run DEXSeq on. Running the analysis on a single machine even with multiple cores is taking prohibitively long. I want to run it on a LSF cluster and distribute the computation across multiple machines(nodes). I have gone through th ...
dexseq lsf distributed computing written 21 months ago by vakul.mohanty10
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Definition of some of the columns in PSCBS segmentation file
... Hello, I used PSCBS and the aroma package to obtain copy number from tumor normal pairs. The code runs fine and I end up with a text file with copy number of segments. I'm however unable to figure out the meaning of some of the columns in the result file(tcnNbrOfLoci, tcnNbrOfSNPs, tcnNbrOfHets, dh ...
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Comment: C: Read counts generated by SGSeq are always 0
... Thank you for all the help Leonard, SGSeq work like a charm now. ...
written 3.0 years ago by vakul.mohanty10
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Comment: C: Read counts generated by SGSeq are always 0
... Thank you that was really informative.  I managed to obtain and run SGSeq 1.5.9., The code runs perfectly for one sample but fails when I input multiple BAM files. Is it possible for me to use one of the apply family of functions and coerce it into the required datastructure?   files$file_bam = Ba ...
written 3.0 years ago by vakul.mohanty10
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Comment: C: Read counts generated by SGSeq are always 0
... Hi I got the R_devel and also found the svn page for SGSeq (https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/SGSeq/), I'm however not familiar with working on the bioc-devel I will be grateful on a pointer to how I can get the package and run it.  Thank you.   ...
written 3.0 years ago by vakul.mohanty10
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Comment: C: Read counts generated by SGSeq are always 0
... Thank you,  I'll give it a shot! ...
written 3.0 years ago by vakul.mohanty10
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Comment: C: Read counts generated by SGSeq are always 0
... I'll make the changes to my BAM files and give it another go. Thank you for the help. Also It will be awesome if you let me know about the changes Thanx! ...
written 3.0 years ago by vakul.mohanty10
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Comment: C: Read counts generated by SGSeq are always 0
... Thank you, I mailed you a text file of the reads from one of my BAM files. ...
written 3.0 years ago by vakul.mohanty10

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