User: vakul.mohanty

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vakul.mohanty240
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9 months ago
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5 years, 6 months ago
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PhD Student at Cincinnati Children's Hospital.

Posts by vakul.mohanty

<prev • 71 results • page 1 of 8 • next >
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PSCBS segmentation file header
... Hello, I'm have used Paired parent specific circular binary segmentation (PSCBS) to segment copy number calls made from SNP6 data and obtain copy numbers as well as LOH calls. I'm however having trouble interpreting some of the columns in the segmentation file. (tcnNbrOfLoci, tcnNbrOfSNPs, tcnNbr ...
snp6 parent spcific copy number cnv aroma written 2.4 years ago by vakul.mohanty240 • updated 2.3 years ago by Eric T.2.5k
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Answer: A: download gene expression data
... GDC (https://gdc-portal.nci.nih.gov/) has breast cancer data from TCGA. You can get the data from there. I think the metadata file of the sample or the clinical data from the breast cancer data have some data whether the sample is ER+ or not. This should help you identify the subset of samples you a ...
written 2.5 years ago by vakul.mohanty240
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Answer: A: Quick and Dirty Gene Network
... Netwalker (https://netwalkersuite.org/) can take your gene names and build interaction networks for you based on multiple curated interaction data sets. It will give you a network and you can play with the outlay, group genes, analyze pathway enrichment. Just load your files select the gene names co ...
written 2.5 years ago by vakul.mohanty240
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Comment: C: variant annotation issue
... You could try annotating with a different annotator and compare results. That could probably help you understand what's going wrong. ...
written 2.5 years ago by vakul.mohanty240
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Answer: A: the question about new TCGA Rnaseq data
... the legacy archive at GDC (https://gdc-portal.nci.nih.gov/) might also have the data your are looking for ...
written 2.5 years ago by vakul.mohanty240
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Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
... Hello, I'm looking to carry out DEXseq (for differential exon usage) and Slueth (differential gene expression) analysis on some TCGA BAM files. As the BAM files can be from different centers and created in different sequencing batches I was looking to control for hidden batch effects using PEER (r ...
batch effects rna-seq differential expression written 2.5 years ago by vakul.mohanty240
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Answer: A: RNASeq detection of TERRA
... This might help: http://www.pnas.org/content/112/46/E6293.long ...
written 2.8 years ago by vakul.mohanty240
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Comment: C: genotype frequency data
... My apologies I missed that some how. True I can think of no annotator that spits out genotype frequencies. ...
written 2.8 years ago by vakul.mohanty240
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Comment: C: genotype frequency data
... ANNOVAR should be able to get you the minor allele frequency from the studies that are part of its database ...
written 2.8 years ago by vakul.mohanty240
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Comment: C: Adding Multiple readgroups to BAM file
... I stuck to the simple split, align and merge approach. it takes a little longer and you have to run multiple instances of the alignment but it works well enough on the cluster. ...
written 2.8 years ago by vakul.mohanty240

Latest awards to vakul.mohanty

Popular Question 10 months ago, created a question with more than 1,000 views. For eQTL analysis on TCGA RNAseq data and SNP6 data
Popular Question 14 months ago, created a question with more than 1,000 views. For eQTL analysis on TCGA RNAseq data and SNP6 data
Popular Question 14 months ago, created a question with more than 1,000 views. For Is it correct to merge TCGA mutation data from multiple centers
Popular Question 21 months ago, created a question with more than 1,000 views. For eQTL analysis on TCGA RNAseq data and SNP6 data
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Where can I find CCLE RNAseq BAM files?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Correlation between miRNA and gene expression data from TCGA

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