User: Vijay Lakhujani

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Posts by Vijay Lakhujani

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Comment: C: Error encountered while running stattest from ballgown
... Hello Vijay Lakhujani! It appears that your post has been cross-posted to another site: Crossposted on biostars.org This is typically not recommended as it runs the risk of annoying people in both communities. ...
written 2.7 years ago by Vijay Lakhujani0
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Answer: A: Error - BSgenomeForge function
... Dear Hervé, This was indeed helpful. Yes, I was using a single file with multiple fasta sequences as my custom genome. Splitting the file into multiple fasta files (chromosome wise) resolved the issue. Thank you very much! While I understand that answering a question as soon as it is posted on th ...
written 3.2 years ago by Vijay Lakhujani0
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Answer: A: How to make my custom genome available in MEDIPS?
... Answering my own question: 1. It looks like it is expected that the forged custom genome will not be listed when you run the command available.genomes() in R. This is because it happened in my case and despite of this, I was able to perform the downstream analysis without any issue. To ensure that ...
written 3.2 years ago by Vijay Lakhujani0
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How many BAM files do I need for MeDIP-seq analysis using MEDIPS bioconductor package?
... I have a generic question about MeDIP-seq analysis using MEDIPS bioconductor package. How many BAM files do I need for the analysis? The example data "MEDIPSData" contains following BAM filles: hESCs.MeDIP.Rep1.chr22.bam(7.6M) hESCs.MeDIP.Rep2.chr22.bam(14M) hESCs.MeDIP.Rep3.chr22.bam(9.1M) h ...
bioconductor medips written 3.2 years ago by Vijay Lakhujani0
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How to make my custom genome available in MEDIPS?
... I am working with MEDIPS bioconductor. I was able to successfully create a custom BEE genome (I know its already there in MEDIPS, but for some reason I wanted to make a different one myself). The genome folder consists of 16 separate fasta files for each chromosomes named like chr1, chr2 and so on. ...
medips written 3.2 years ago by Vijay Lakhujani0
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Answer: A: Installing problem Bioconductor
... Hi, Looks like you are working in windows OS. Check if you have read/write permission for the directory C:/Program Files/R/R-3.3.1/library. To set read/write permission: Right-click the folder (C:/Program Files/R/R-3.3.1/library) , click Properties, and then click the Security tab. Click ...
written 3.3 years ago by Vijay Lakhujani0
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Error - BSgenomeForge function
... Hi, I am using the MEDIPS package for MeDIP-seq analysis where I am trying to create a custom genome for Vigna radiata (not already present in the package) and I am referring to below manual for guidance: https://www.bioconductor.org/packages/devel/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pd ...
bsgenomeforge written 3.3 years ago by Vijay Lakhujani0

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