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ONT_pilot_gitlab
Commits
9c650220
Commit
9c650220
authored
Apr 21, 2021
by
Valentina Galata
Browse files
notes: metap: added ben's cmds; updated readme (issue
#127
)
parent
02b4f793
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README.md
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9c650220
...
...
@@ -115,6 +115,8 @@ Note that the workflow will create additional output files not necessarily requi
This workflow creates various summary files, plots and an HTML report for a sample using the output of the main workflow.
Note: How the metaP peptide/protein reports were generated from raw metaP data is described in
`notes/gdb_metap.md`
.
-
config:
-
sample configs used for the main workflow
-
workflow:
`workflow_report/`
...
...
@@ -141,10 +143,11 @@ snakemake -s workflow_figures/Snakefile --cores 1 --configfile config/fig.yaml -
# Notes
Notes
about manu
al analyses done using the generated data.
Notes
for manual/addition
al analyses done using the generated data.
-
`gdb_metap.md`
: how the metaP reports were generated
-
`gdb_mmseqs2_highconf.md`
: sample GDB, "high-confidence" proteins and protein clusters (assembly intersection and metaT cov.)
-
`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
-
`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
notes/gdb_metap.md
0 → 100644
View file @
9c650220
Code used to generate metaP reports which are included in the report workflow.
The reports were generated for
-
proteins from each assembly separately
-
all proteins from all assemblies together
```
bash
##Generate parameters file
java-cp SearchGUI-3.3.20.jar eu.isas.searchgui.cmd.IdentificationParametersCLI
\
-out
"params.par"
\
-db
"database.fasta"
\
-prec_tol
10
\
-prec_ppm
1
\
-frag_tol
15
\
-frag_ppm
1
\
-digestion
0
\
-enzyme
"Trypsin"
\
-specificity
0
\
-mc
2
\
-fixed_mods
"Carbamidomethylation of C"
\
-variable_mods
"Oxidation of M"
\
-min_charge
2
\
-max_charge
4
\
-fi
"b"
\
-ri
"y"
\
-min_isotope
0
\
-max_isotope
1
\
-import_peptide_length_min
7
\
-import_peptide_length_max
60
\
-xtandem_noise_suppr
0
\
-xtandem_quick_acetyl
1
\
-xtandem_quick_pyro
1
\
-xtandem_refine
1
\
-msgf_instrument
1
\
-msgf_fragmentation
1
\
-msgf_protocol
0
\
-msgf_min_pep_length
7
\
-msgf_max_pep_length
60
\
-msgf_num_ptms
2
\
-comet_num_ptms
2
#SearchGUI search
java
-cp
SearchGUI-3.3.20.jar eu.isas.searchgui.cmd.SearchCLI
\
-spectrum_files
"MGF_DIR"
\
-output_folder
"OUT_DIR"
\
-id_params
"params.par"
\
-xtandem
1
\
-msgf
1
\
-comet
1
\
-andromeda
0
\
-output_default_name
"Sample_Name"
\
-output_option
0
\
-output_data
1
\
-output_date
1
#PeptideShaker analysis
java
-cp
PeptideShaker-1.16.45.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI
\
-experiment
"Sample_Name"
\
-sample
"1"
\
-replicate
"1"
\
-identification_files
"SearchGUI_Outpit"
\
-out
"Sample_Name.cpsx"
\
-zip
"Sample_Name.cpsx.zip"
#PeptideShaker reports.
java
-cp
PeptideShaker-1.16.45.jar eu.isas.peptideshaker.cmd.ReportCLI
\
-in
"Sample_Name.cpsx.zip"
\
-out_reports
"OUT_DIR"
\
-reports
6,9
#Mzid Generation
java
-cp
PeptideShaker-1.16.45.jar eu.isas.peptideshaker.cmd.MzidCLI
\
-in
"Sample_Name.cpsx.zip"
\
-output_file
"Sample_Name.mzid"
\
-contact_first_name
Benoit
\
-contact_last_name
Kunath
\
-contact_email
benoit.j.kunath@gmail.com
\
-contact_address
avenue de l’Université 7 Belval Luxembourg
\
-organization_name
LCSB
\
-organization_email
benoit.kunath@uni.lu
\
-organization_address
avenue de l’Université 7 Belval Luxembourg
```
\ No newline at end of file
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