Re-run STAR aligner using Dungeness crab and MEGAN-scrubbed RNASeq data

[laurahspencer]

@ggoetznoaa get scrubbed RNASeq data from @kubu4

[kubu4]

Alrighty, read extractions have been performed.

FastQs are here (*.fq.gz):

• https://gannet.fish.washington.edu/Atumefaciens/20230730.mmag-megan_reads/

MD5 checksums file:

• https://gannet.fish.washington.edu/Atumefaciens/20230730.mmag-megan_reads/checksums.md5

Notebook:

• https://robertslab.github.io/sams-notebook/2023/07/30/Read-Extractions-M.magister-MEGAN-FastA-to-FastQ-Arthropoda-and-Unassigned-Reads.html

@ggoetznoaa - Here's a direct link to Jupyter Notebook (NB Viewer) on how to use MEGAN FastAs to get corresponding reads from original FastQs. Let me know if you have any questions/concerns!

• https://nbviewer.org/github/RobertsLab/code/blob/master/notebooks/sam/20230730-mmag-megan-fasta_to_fastq.ipynb

[ggoetznoaa]

Ran this using the script run.star_align_megan6_gensas.v1.sh, alignment stats found in spreadsheet under tab "STAR MEGAN6 GENSAS"