This is the workflowr site for my Net-seq project. I will have all of the data, code, and analysis here.

Set-up for mappping my libraries:

• Setting up conda environment

• Setting up config and snake files

Initial data exploration:

• Initial data exploration for NetSeq1 libary

• Explore read lengths that are mapping

• Explore the UMI usage in the NetSeq1 library

• Use the genomation package to vizualize genome features and see overlap with Net-seq1

• Exploration of read counts per gene

• Reformat gene counts for ggplot2 data analysis

• Explore read counts per genome bin

• Create IGV browser style plots

Initial analysis for Net-3:

• Net-3 Initial exploration

Net-pilot analysis:

• Update snakefile for pilot analysis

• Create blacklist to filter reads

Cell Growth analysis:

• Initial plots on growth

Exploration of the 3` seq and ApA sites:

• Look for read enrichment at ApA sites

• UTR coverage analysis

• Look at enrichment using Deep tools

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