Read Extractions - M.magister MEGAN Arthropoda and Unassigned Reads to FastA

Metacarcinus magister
Dungeness crab
MEGAN
2023
DuMOAR
Author

Sam White

Published

July 26, 2023

After converting DIAMOND BLASTx/MEGAN DAA files to RMA6 and looking at the taxonomic breakdown of each sample (notebook entry), it was decided we should extract reads from Arthropoda (and all taxonomies below) and all Unassigned reads from each sample. To do so, I used MEGAN6 Community Edition.

Unfortunately, the Community Edition doesn’t provide command-line tools to perform this task, so it had to be done via the GUI. As such, it took a couple of days to go through all of these. See the MEGAN log file for a computer-generated record of what was selected in the GUI for each file. Reads are extracted as FastAs. After FastA extraction, I’ll go back to the trimmed FastQs and use the FastAs to extract reads in FastQ format.

RESULTS

Output folder:

MEGAN Log

  • MEGAN-log.txt

    • Since extractions were performed using the GUI, this file is the only computer-generated record of what was selected for extraction.

FastA Files