fo21 March 2018

All analyses are explained in the html version of an R markdown file. See Salvinia_Analysis_Pipeline.html

A file containing all GBS barcodes is also included (Salv.Bcode.txt)

The raw data are in compressed fastq files that have been split for ease of data transfer. Files are xaa_Salvinia.fastq.zip though xan.etc. These need to be unzipped and concatenated as follows.

At command line:

gunzip xa*.Salvinia*

(Wait for this to complete). Then:

cat xa*.Salvinia* > Allenr_01_S4_L008_R1_001.fastq

Then rezip it:

gzip gomp001_NoIndex_L003_R1_001.fastq.gz (or however you wish to name file)

This will recreate the file and correct filename for all downstream analyses, which can be viewed in the R Markdown file or the html version of that.

Any issues, please contact Paul.wolf11@gmail.com or carol.rowe666@gmail.com