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Welcome to the RNA-Seq-Splicing-Analysis-Pipeline wiki!

Software requests:

• WASP
• MatrixQTL
• LeafCutter (complete)

Goal:

• Build a pipeline that quantifies RNA splicing and performs sQTL mapping

Input:

• .bam files (aligned RNA-Seq reads)

Output:

1. splicing quantifications (intron excision ratios)
2. sQTL mapping results

Week	Brianne	Ally	Ryan	Group Goals	Due/Events
Feb 20				Assign Basic roles, Create a basic Timeline	Weekly meeting
Feb 26	WASP SOP	FastQTL/MatrixQTL SOP	Leafcutter SOP	Research our software, as well as sQTLs and .BAM files. Be prepared to explain at weekly meeting. Upload all papers and notes if available to git before Repo check**	Mar 1st, Repo Check #1
Mar 5	slides - implementation plan	slides - introduction	slides - introduction/weekly benchmarks	Begin and complete group presentation. Practice with our softwares and play with BAM files	Spring Break
Mar 12	perform more extensive research on WASP, test with toy data	practice with toy data set in FastQTL	Practice LeafCutter with toy data	Meet Monday before to practice the presentation.	Group presentations Mar 15
Mar 19	begin writing code to utilize software as necessary	begin practicing with MatrixEQTL	alter leafcutter output to be acceptable for MatrixEQTL input	begin implementing code	Repo Check Mar 22
Mar 26	make bash script	make bash script	make bash script	test scripts using Dr. Wheeler's data	5 Minute group presentation Mar 29
Apr 2	finish debugging code	finish debugging	finish debugging	unify bash scripts into one pipeline
Apr 9	finish debugging pipeline	finish debugging pipeline	finish debugging pipeline	automate pipeline as much as possible
Apr 16	assemble group presentation	assemble group presentation	assemble group presentation		Finish Project Apr 17. Repo Check Apr 19
Apr 23	final presentation	final presentation	final presentation		Final Presentations Apr 24/26