CNV analysis pipeline using Gistic2
Dear every body, I downloaded level 3 CNV data from TCGA (segmented files). I am going to use Gistic2 to identify recurrent CNVs ? There are some command line in different links for it. https://gatkforums.broadinstitute.org/firecloud/discussion/8254/gistic2-0 But I dont know where to download Gistic2 and where to run command line instructions??
I also checked this link: How to extract the list of genes from TCGA CNV data but runGAIA() function need a lot memory to run. and I got allocation error. It used 100 gig bite RAM in one minute.
1 answer
Log in to answer this question.
More posts like this
-
Merging segment CNV files
written by avelarbio46 •
-
List index out of range
written by Samiah •
-
Picard tools - Cigar element being constructed with negative length
written by Andy •
-
SRA files bulk downloads
written by S AR
-
cnv-seq running error
written by reza
-
Aligning multiple paired-end samples tophat2 command line
written by nash.claire
-
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
written by Chirag Nepal
-
VariantAnnotation: error from readVcf command
written by pifferdavide
-
problem running local blast after downloading on MacOSX
written by gusmonksu •
-
Memory Problems Running Gatk Printreads
written by ajc8 •
