Commit 9c650220 authored by Valentina Galata's avatar Valentina Galata
Browse files

notes: metap: added ben's cmds; updated readme (issue #127)

parent 02b4f793
......@@ -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 manual analyses done using the generated data.
Notes for manual/additional 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)~~
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- `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)
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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
```
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