/gannet/Atumefaciens/20190416_metagenomics_pgen_blastn

Gene annotation using BLASTn on Mox with pH-specific (pH=7.1 and pH=8.2) MetaGeneMark predictions.

Followed by creation of Krona plot displaying taxonomic makeup of each pH treatment.

Input FastA files were from MetaGeneMark gene predictions on 20190416:

https://robertslab.github.io/sams-notebook/2019/04/16/Metagenomics-Gene-Prediction-P.generosa-Water-Samples-Using-MetaGeneMark-on-Mox-to-Compare-pH-Treatments.html



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FILES

- 20190416_metagenomics_pgen_blastn.sh: SBATCH script to run MetaGeneMark on Mox.

- input.fasta.list.txt: List of input FastAs used with MetaGeneMark.

- krona_megahit_MGM_blastn.html: Interactive KronaTools plot showing taxonomic makeup of both treatments. Opens in browser.

- krona_megahit_MGM_blastn.html.files: KronaTools output files for running interactive KronaTools plot.

- krona_stderr.txt: Standard error file from KronaTools.

- krona_stdout.txt: Standard out file from KronaTools.

- krona_tax_plots_blast.sh: Bash script for running KronaTools on Sam's computer (swoose).

- pH71.blastn.outfmt6: pH=7.1 BLASTn results; output format 6, plus staxids.

- pH71.krona_tax.lst: pH=7.1 taxonomy list, extracted from BLAST output file. Required input for KronaTools. See krona_tax_plots_blast.sh for info on how list is assembled.

- pH82.blastn.outfmt6: pH=8.2 BLASTn results; output format 6, plus staxids.

- pH82.krona_tax.lst: pH=8.2 taxonomy list, extracted from BLAST output file. Required input for KronaTools. See krona_tax_plots_blast.sh for info on how list is assembled.

- slurm-754024.out: SLURM output file (stderr/stdout).

- system_path.log: Log file of items in Sam's Mox system $PATH.



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Notebook:

https://robertslab.github.io/sams-notebook/2019/04/16/Metagenomics-Annotation-P.generosa-Water-Samples-Using-BLASTn-on-Mox-and-KronaTools-Visualization-to-Compare-pH-Treatments.html