Raw reads
In March 2021, we received eight files with sequence reads. Four of these contain the 1x100bp reads, because four lanes (pools) were used on the instrument. Four of these because CU unnecessarily ran indexing reads on the fragments. I deleted these nonsense files. The four files with the raw reads of interest are (these are in /project/evolgen/data/local/alfalfa/alf1GBS_NS1_mar21/, with original files in /project/microbiome/data/seq/alfalfa/GBS/Alf1GBS_NS1/).
Pool1_S1_L001_R1_001.fastq (20 GB) – 416,256,593 reads (99 GBytes uncompressed)
Pool2_S2_L002_R1_001.fastq.gz (20 GB) – 405,613,054 reads (97 GBytes uncompressed)
Pool3_S1_L001_R1_001.fastq.gz (23 GB)
Pool4_S2_L002_R1_001.fastq.gz (19 GB)
I used unpigz.sh to decompress the fastq files, because our parser does not read from gzipped files.
Demultiplexing
...
See README.md in https://bitbucket.org/buerklelab/alfalfagbs/src/main/