Manohar Chakrabarti, PI/Scientist-1/AG/Department of Plant and Soil Sciences

Introduction to Chakrabarti Lab:

We focus on transcriptional, post-transcriptional, and epigenetic regulation of gene expression under different developmental and physiological processes in diverse plant species, including redclover, tall fescue, sorghum, and tobacco (Nicotiana tabacum). At the transcriptional level, we routinely conduct RNAseq experiments, while at the post-transcriptional level we use our in house PATseq pipeline to look at genome-wide distribution of alternative polyadenylation. At the epigenetic level, we are conducting whole genome bisulfite sequencing experiments.

Analyzing WGBS Experiment Using Tobacco Leaves

In LCC, we would like to analyze the data from a WGBS (whole genome bisulfite sequencing) experiment using tobacco leaves. Data analysis for this project, can’t be completed using the computational resources available at the Department of Plant and Soil Sciences. Hence, we are requesting user privilege on the LCC cluster. CPU time requested: 5 days.

Personnel:

Dr.Manohar Chakrabarti, PI, Scientist-1

Software:

R, Bioconductor, homebrew, bioconda, fastqc, trim-galore, samtools, hisat2, Bismark, multiQC, methylKit R package, BEDOPS tool.

All of these tools are open source and already available in LCC cluster.

UK and non-UK collaborators:

None

Grants:

Publications:

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