27 February 2019

Data posted here includes:
1. markdown files detailing analyses of amplicon data (Pteridium_amplicon_pipeline.Rmd)
2. Raw amplicon sequence data as a compressed file of fastq reads (Pteridium_amplicon.zip)
3. Compressed folder of final clustered/filtered fasta sales fro amplicon sequencing:trim99_pandaseq_merged_reads.zip
4. Pteridium_GBS_Tutorial.html - pipeline for analysis of GBS data (also see https://github.com/sylviakinosian/Pteridium_GBS_Pipeline)
5. The raw data are in compressed fastq files that have been split for ease of data transfer. Files are xaa_Pter_GBS.fastq.gz though xan.etc. These need to be unzipped and concatenated as follows.

At command line:

gunzip xa*.Pter*.fastq

(Wait for this to complete). Then:

cat xa*.Pter* > Pter_01_S17_L002_R1_001.fastq

Then rezip it:

gzip Pter_01_S17_L002_R1_001.fastq

This will recreate the file and correct filename for all downstream analyses, which can be viewed here: https://github.com/sylviakinosian/Pteridium_GBS_Pipeline. Or see Pteridium_GBS_Tutorial.html

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