-
CentC Project Workflow *
By: Paul Bilinski, UC Davis, 2013
Original, large data files can be found on: http://figshare.com/account/projects/124
- Extract all CentC's from the maize reference genome (version 2) -The original CentC sequences (Genbank + Nagaki et al 2003 Study) are in
CentC_Seq_Originals.fasta
-Use the reverse complimented sequences for BLASTing.
-Follow instructions in the README_blast_anno.txt
-The DNA distance matrices can be generated using PHYLIP software package, DNADIST function. This project was run using PHYLIP 3.69. To regenerate my dna distance matrices, I first performed 7 muscle alignments of the sequences I wanted to have in the distance matrix (for example, all CentC from chromosome 2 or 5). This was performed in Geneious's muscle. Then the alignment was fed to the dnadist.
-Execute the Spagedi analyses given the distance matrices and text files in the spagedi manual. These analyses were run with SPAGeDi 1.3a.
-Use these distances to generate the figure in the text
-The scripts you will need are: Making_Chr_Dist_Figures.R ExtractforSpagedi.pl Extract_Seq_Pos.pl Extract_Seq.pl
- Circos
-Follow Kevin's Circos code in the Readme generated from his email. The necessary files are POS_chrAll.txt and the subgenome assignments from Schnable.
- PacBio Tandem CentC Parsing in long reads
-Filtered data for long reads with CentC blast hits in is the PacBio folder
-Follow the Readme to calculate tandem counts seen in supplementary table
- CentC abundance simulations with Mosaik
-Code available on Kevin Distor's Github https://github.com/kddistor/dnasims
- Mapping Abundance with Mosaik
-Mosaik itself is zipped into this repo. Open and install.
-Following manual and our parameters, you can map against the reference of all of the CentC's in the maize genome. Results are on this repo.
- Diversity simulations (to show homoplasy is possible)
-Simple code in the diversity sims, execute and observe how many total shared mutations of frequency occur
- Tracy Widom Analyses
-In the PCoA_Analyses directory you will find the following files:
ConvertPhylipMatrixtoCSV.pl: perl script to make phylip files into csv matrix Original_centc_DNADIST.csv: test matrix of 218 original CentC twtable.txt: Joosts table
-Use these and the twcentc.rmd to recalculate the values
-A test matrix with the original 218 sequences is provided as well.
- Gaby's CHIP results
-Performed in with Bowtie, mapped against CHIP reads from paper cited in text.
- Cluster Distance Adjusting
-Using the AdjustCluster.pl and ClusterNeighbors_forscript.csv, you can calculate various cluster distances
-The Code to do so is at the start of the perl script, or here #for i in {1..20}; do BP=$(( $i*1000 )); perl AdjustCluster.pl $BP 10000; done #code to execute it for a lot of diff distances
If I have forgotten any analysis, please contact me at my UCDAVIS email and I will be sure to upload it!