PacBio data came from Wisconsin
Raw data at https://owl.fish.washington.edu/nightingales/S_namaycush/LakeTrout/
have 4 lean and 4 siscowets
they were run in three pools
Pool 1.
Lean FA047 bc2041 TATGATCACTGAGTAT.
Siscowet FA097 bc2071 CGAGTCTAGCGAGTAT.
Siscowet FA099 bc2072 TATCAGTAGTGAGTAT.
Pool 2.
Lean FA094 bc2069 TCTATGACATGAGTAT.
Lean FA095 bc2070 TACTGCTCACGAGTAT.
Siscowet FA100 bc2073 ATCACTAGTCGAGTAT.
Pool 3.
Lean FA092 - bc2068 ACTACGTGATGAGTAT.
Siscowet FA253 - bc2096 ATGTACTAGTGAGTAT.
TLDR
| Type | Sample ID |
|---|---|
| Lean | bc2041 |
| Lean | bc2068 |
| Lean | bc2069 |
| Lean | bc2070 |
| Siscowet | bc2071 |
| Siscowet | bc2072 |
| Siscowet | bc2073 |
| Siscowet | bc2096 |
Fastq files @ https://gannet.fish.washington.edu/v1_web/owlshell/bu-github/project-lake-trout/data/pacbio-reads/fastq2/
The first two pools arrived as Bams, and Sam demultiplexed. https://robertslab.github.io/sams-notebook/posts/2025/2025-10-23-Demultiplexing---S.namaychush-PacBio-Sequencing-Using-Lima/
The third pool arrived demultiplexed.
Sam generated corresponding fastq files
NanoPlot
For each of the 8 files ran
/opt/anaconda/anaconda3/envs/nanoplot_env/bin/NanoPlot \
-t 40 \
--fastq ../data/pacbio-reads/fastq2/m84082_250614_101514_s4.hifi_reads.demux.bc2069--bc2069.fastq.gz \
-o ../analyses/08-nanoplot/bc2069 \
--prefix bc2069_which created
MultiQC
after all were complete ran multiqc
multiqc ../analyses/08-nanoplot/ -o ../analyses/08-multiqc