Closed ndreey closed 1 year ago
Because the scp
command did not work when trying to get the P_ziji file to local I will use the A. thaliana reference genome we just removed as practice data, GCF_000001735.4_TAIR10.1_genomic.fna.gz
.
Because NGSNGS is supposedly faster and created by bioinformaticians at KU I will use this simulation program instead of ART
EDIT
The scp
did not work as i was running the command from WSL, when i ran the same code in pwsh
it worked. I assume my WSL is not set up with a ssh-agent
and is thus the reason for not working.
Determine how to set seed
and have NGSNGS generate reads of P_zinji
three times so we don't dilute with same reads across all samples (maybe four or five times??).
The practice reference had seven 5 chromosomes, one plastid, and one chloroform genome sequence. I split the file to only hold the chloroform sequence. After many tries, I am able to create both SE and PE fastq reads.
Single End
$ngsngs -i data/references/ncbi-genomes-2023-03-08/TAIR10_chloro.fna -c 3 -f fq -l 100 -seq SE -t 2 -q1 data/references/AccFreqL150R1.txt -o ninja2
Paired End$ngsngs -i data/references/ncbi-genomes-2023-03-08/TAIR10_chloro.fna -c 3 -f fq -l 100 -seq PE -t 2 -q1 data/references/AccFreqL150R1.txt -q2 data/references/AccFreqL150R2.txt -o ninja3
The question lies now in understanding the quality profile file that is required.
Update:
What dawned on me, though, is that if I were to dilute a 4.5GB mock data file to reach 90% P. zijinensis the file would become ~45GB??. Not good..
Closing as i will run CAMISIM instead.
Create in silico NGS data of Platanthera spp. using the reference genome. Either ART or NGSNGS will be used