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ONT_pilot_gitlab
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b3934134
Commit
b3934134
authored
Apr 19, 2021
by
Valentina Galata
Browse files
readme: updated notes; added file for results archive
parent
eeac8cad
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README.md
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b3934134
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@@ -143,7 +143,8 @@ snakemake -s workflow_figures/Snakefile --cores 1 --configfile config/fig.yaml -
Notes about manual analyses done using the generated data.
-
`gdb_mmseqs2_uniq_metat.md`
: sample GDB, unique genes and their metaT coverage
-
`gdb_mmseqs2_highconf.md`
: sample GDB, "high-confidence" proteins and protein clusters (assembly intersection and metaT cov.)
-
`gdb_rgi_aro3004454_flye.md`
,
`gdb_rgi_other.md`
: sample GDB, RGI examples for diff. between SR/Hy and LR, and metaT coverage
-
`gdb_barrnap_metat.md`
: sample GDB, metaT cov. of some predicted rRNA genes (barrnap)
\ No newline at end of file
-
`gdb_rgi_aro3004454_flye.md`
: sample GDB, an RGI example for diff. between SR/Hy and LR, and metaT coverage
-
~~
`gdb_mmseqs2_uniq_metat.md`
: sample GDB, unique genes and their metaT coverage~~
-
~~
`gdb_rgi_other.md`
: sample GDB, other RGI examples for diff. between SR/Hy and LR, and metaT coverage~~
-
~~
`gdb_barrnap_metat.md`
: sample GDB, metaT cov. of some predicted rRNA genes (barrnap)~~
\ No newline at end of file
README_ARCHIVE.md
0 → 100644
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b3934134
# About
Results archive created for manuscript submission.
# Archived files
Abbreaviations and names:
-
sample names: Zymo, NWC, GDB, Rumen
-
SR: short-read (data)
-
LR: long-read (data)
-
Hy: hybrid (SR+LR)
-
metaG: metagenomic data
-
metaT: metatranscriptomic data
-
only for GDB
-
metap: metaproteomic data
-
only for GDB
For each sample, the following files were saved (in
`<sample>/results/`
):
-
preprocessing stats:
-
SR (metaG/metaT), FastP stats:
`preprocc/*/sr/fastp.*`
-
SR/LR (metaG/metaT, GDB), bbmap stats:
`preproc/*/*/bbmap.*`
-
reads QC:
-
SR (metaG/meetaT), FastQC:
`qc/*/sr/*_fastqc.zip`
-
LR, NanoStats:
`qc/*/lr/NanoStats.*`
-
assembly
-
"raw" contigs:
`assembly/*/*/ASSEMBLY.fasta`
-
polished contigs:
`assembly/*/*/ASSEMBLY.POLISHED.fasta`
(for LR and Hy only)
-
polishing rounds:
`assembly/*/*/POLISHING_*/ASSEMBLY.fasta`
-
assembly mapping
-
BAM files:
`mapping/*/*/*/ASSEMBLY.POLISHED.*.bam`
-
mapping rate summary stats:
`mapping/*/mappability.tsv`
-
annotation
-
protein prediction w/ Prodigal
-
FAA FASTA file:
`annotation/prodigal/*/*/proteins.faa`
-
summary (gene counts):
`annotation/prodigal/summary.gene.counts.tsv`
-
summary (summary gene length):
`annotation/prodigal/summary.gene.length.tsv`
-
AMR prediction w/ RGI (CARD)
-
RGI output:
`annotation/rgi/*/*/rgi.txt`
-
summary:
`annotation/rgi/summary.tsv`
-
rRNA gene prediction w/ barrnap
-
GFF file:
`annotation/barrnap/*/*/*.gff`
-
summary:
`annotation/barrnap/summary.tsv`
-
analysis:
-
assembly quality stats w/ QUAST
-
QUAST report:
`analysis/quast/*/*/report.tsv`
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sumamry:
`analysis/quast/summary_report.tsv`
-
analysis w/ Mash:
`analysis/mash/contigs.*`
(sketch and distances)
-
DIAMOND search in UniProt database
-
DIAMOND hits:
`analysis/diamond/*.tsv`
-
summary:
`analysis/diamond/summary.db.tsv`
-
protein clustering w/ mmseqs2
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clusters:
`analysis/mmseqs2/clusters.tsv`
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summary:
`analysis/mmseqs2/summary.tsv`
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extra data/analysis for GDB:
-
metaP reports:
`metap/20210323/*_Default_Peptide_Report.txt`
,
`metap/20210323/*_Default_Protein_Report.txt`
-
AMR/metaT analysis:
`report/amr.tsv`
-
"high-confidence" proteins:
`report/mmseqs2_highconf.tsv`
-
metaT cov. of exclusive proteins:
`report/mmseqs2_uniq.tsv`
-
metaP-based summary:
`report/metap.txt`
README_REPROD.md
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b3934134
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@@ -4,10 +4,6 @@ Notes for those trying to reproduce the results from the publication.
# Setup
Download
-
the code archive from XXX and extract it
-
GDB data from XXX
Install
`conda`
and create the main
`snakemake`
environment (see
`README.md`
).
Clone
`OPERA-MS`
repository
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