diff --git a/.gitattributes b/.gitattributes index cd142a99c5eb2b48fbce8e3d6b9897063cabd5f0..32a069a88770ccbf95d845c596322e4f69924310 100644 --- a/.gitattributes +++ b/.gitattributes @@ -571,3 +571,125 @@ external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFin external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/OrthoFinder/Results_analysis_2953776/WorkingDirectory/clusters_OrthoFinder_I1.5.txt_id_pairs.txt filter=lfs diff=lfs merge=lfs -text external/orthogroups/orthofinder/results/Results_Oct13/WorkingDirectory/SequenceIDs.txt filter=lfs diff=lfs merge=lfs -text external/orthogroups/sonicpd/graph_only/not_assigned_genes.ortholog_groups.tsv filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper06/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper09/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper10/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper10/transcriptome_clstr.pep.clstr filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper12/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper12/transcriptome_clstr.pep.clstr filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper20/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper20/transcriptome_clstr.pep.clstr filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper23/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper23/transcriptome_clstr.pep.clstr filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper25/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper25/transcriptome_clstr.pep.clstr filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper26/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper26/transcriptome_clstr.pep.clstr filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper27/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper27/transcriptome_clstr.pep.clstr filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper32/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper32/transcriptome_clstr.pep.clstr filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper54/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper55/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper56/transcriptome_clstr.pep filter=lfs diff=lfs merge=lfs -text +interim/cdhit/piper56/transcriptome_clstr.pep.clstr filter=lfs diff=lfs merge=lfs -text +interim/mzmine/fbmn.mgf filter=lfs diff=lfs merge=lfs -text +interim/mzmine/network_fbmn.graphml filter=lfs diff=lfs merge=lfs -text +interim/mzmine/network_iimn.graphml filter=lfs diff=lfs merge=lfs -text +interim/mzmine/sirius.mgf filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper06/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text 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merge=lfs -text +interim/transxpress/piper10/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper10/annotations/signalp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper10/annotations/sprotblastp_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper10/annotations/targetp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper10/annotations/tmhmm_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper10/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper10/transcriptome.pep filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper10/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper12/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper12/annotations/signalp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper12/annotations/sprotblastp_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper12/annotations/targetp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper12/annotations/tmhmm_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper12/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper12/transcriptome.pep filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper12/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper20/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper20/annotations/signalp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper20/annotations/sprotblastp_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper20/annotations/targetp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper20/annotations/tmhmm_pep.out filter=lfs diff=lfs merge=lfs -text 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-text +interim/transxpress/piper25/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper25/annotations/signalp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper25/annotations/sprotblastp_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper25/annotations/targetp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper25/annotations/tmhmm_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper25/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper25/transcriptome.pep filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper25/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper26/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper26/annotations/signalp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper26/annotations/sprotblastp_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper26/annotations/targetp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper26/annotations/tmhmm_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper26/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper26/transcriptome.pep filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper26/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper27/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper27/annotations/signalp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper27/annotations/sprotblastp_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper27/annotations/targetp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper27/annotations/tmhmm_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper27/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper27/transcriptome.pep filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper27/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper32/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper32/annotations/signalp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper32/annotations/sprotblastp_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper32/annotations/targetp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper32/annotations/tmhmm_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper32/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper32/transcriptome.pep filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper32/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper54/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper54/annotations/sprotblastp_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper54/annotations/targetp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper54/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper54/transcriptome.pep filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper54/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper55/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper55/annotations/sprotblastp_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper55/annotations/targetp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper55/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper55/transcriptome.pep filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper55/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper56/annotations/pfam_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper56/annotations/signalp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper56/annotations/sprotblastp_orfs.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper56/annotations/targetp_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper56/annotations/tmhmm_pep.out filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper56/transcriptome.fasta filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper56/transcriptome.pep filter=lfs diff=lfs merge=lfs -text +interim/transxpress/piper56/transcriptome_expression_isoform.tsv filter=lfs diff=lfs merge=lfs -text diff --git a/README.md b/README.md index f64ec9943f1a8408ac84420a88d59432219419e9..39eaa8ec979879e02be6d6b8dd88dc4d01c2cb9b 100644 --- a/README.md +++ b/README.md @@ -24,15 +24,15 @@ data/ │ ├── lcms/ │ │ ├── rawfiles/ # LC-MS raw files, mzML (140 files) │ │ └── metadata.tsv # sample metadata, read by MZmine -│ └── rnaseq/piperNN/ # transXpress output, one folder per sample ID (13) -│ ├── transcriptome.fasta # de novo assembly -│ ├── transcriptome.pep # predicted proteins -│ ├── transcriptome_expression_isoform.tsv -│ ├── busco_report.txt -│ └── annotations/ # Pfam, BLASTp, SignalP, TargetP, TMHMM ├── interim/ -│ ├── lcms_mzmine/ # MZmine output: feature table, MS/MS spectra (.mgf), annotations, networks (.graphml) -│ └── rnaseq_clstr/piperNN/ # CD-HIT clustered proteomes +│ ├── mzmine/ # MZmine output: feature table, MS/MS spectra (.mgf), annotations, networks (.graphml) +│ ├── transxpress/piperNN/ # transXpress output, one folder per sample ID (13) +│ │ ├── transcriptome.fasta # de novo assembly +│ │ ├── transcriptome.pep # predicted proteins +│ │ ├── transcriptome_expression_isoform.tsv +│ │ ├── busco_report.txt +│ │ └── annotations/ # Pfam, BLASTp, SignalP, TargetP, TMHMM +│ └── cdhit/piperNN/ # CD-HIT clustered proteomes ├── external/ │ ├── molecular_networks/ │ │ └── gnps2/ # GNPS2 feature-based molecular networking results diff --git a/interim/rnaseq_clstr/piper06/transcriptome_clstr.pep b/interim/cdhit/piper06/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper06/transcriptome_clstr.pep rename to interim/cdhit/piper06/transcriptome_clstr.pep diff --git a/interim/rnaseq_clstr/piper06/transcriptome_clstr.pep.clstr b/interim/cdhit/piper06/transcriptome_clstr.pep.clstr similarity index 100% rename from interim/rnaseq_clstr/piper06/transcriptome_clstr.pep.clstr rename to interim/cdhit/piper06/transcriptome_clstr.pep.clstr diff --git a/interim/rnaseq_clstr/piper09/transcriptome_clstr.pep b/interim/cdhit/piper09/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper09/transcriptome_clstr.pep rename to interim/cdhit/piper09/transcriptome_clstr.pep diff --git a/interim/rnaseq_clstr/piper09/transcriptome_clstr.pep.clstr b/interim/cdhit/piper09/transcriptome_clstr.pep.clstr similarity index 100% rename from interim/rnaseq_clstr/piper09/transcriptome_clstr.pep.clstr rename to interim/cdhit/piper09/transcriptome_clstr.pep.clstr diff --git a/interim/rnaseq_clstr/piper10/transcriptome_clstr.pep b/interim/cdhit/piper10/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper10/transcriptome_clstr.pep rename to interim/cdhit/piper10/transcriptome_clstr.pep diff --git a/interim/rnaseq_clstr/piper10/transcriptome_clstr.pep.clstr b/interim/cdhit/piper10/transcriptome_clstr.pep.clstr similarity index 100% rename from interim/rnaseq_clstr/piper10/transcriptome_clstr.pep.clstr rename to interim/cdhit/piper10/transcriptome_clstr.pep.clstr diff --git a/interim/rnaseq_clstr/piper12/transcriptome_clstr.pep b/interim/cdhit/piper12/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper12/transcriptome_clstr.pep rename to interim/cdhit/piper12/transcriptome_clstr.pep diff --git a/interim/rnaseq_clstr/piper12/transcriptome_clstr.pep.clstr b/interim/cdhit/piper12/transcriptome_clstr.pep.clstr similarity index 100% rename from interim/rnaseq_clstr/piper12/transcriptome_clstr.pep.clstr rename to interim/cdhit/piper12/transcriptome_clstr.pep.clstr diff --git a/interim/rnaseq_clstr/piper20/transcriptome_clstr.pep b/interim/cdhit/piper20/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper20/transcriptome_clstr.pep rename to interim/cdhit/piper20/transcriptome_clstr.pep diff --git a/interim/rnaseq_clstr/piper20/transcriptome_clstr.pep.clstr b/interim/cdhit/piper20/transcriptome_clstr.pep.clstr similarity index 100% rename from interim/rnaseq_clstr/piper20/transcriptome_clstr.pep.clstr rename to interim/cdhit/piper20/transcriptome_clstr.pep.clstr diff --git a/interim/rnaseq_clstr/piper23/transcriptome_clstr.pep b/interim/cdhit/piper23/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper23/transcriptome_clstr.pep rename to interim/cdhit/piper23/transcriptome_clstr.pep diff --git a/interim/rnaseq_clstr/piper23/transcriptome_clstr.pep.clstr b/interim/cdhit/piper23/transcriptome_clstr.pep.clstr similarity index 100% rename from interim/rnaseq_clstr/piper23/transcriptome_clstr.pep.clstr rename to interim/cdhit/piper23/transcriptome_clstr.pep.clstr diff --git a/interim/rnaseq_clstr/piper25/transcriptome_clstr.pep b/interim/cdhit/piper25/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper25/transcriptome_clstr.pep rename to interim/cdhit/piper25/transcriptome_clstr.pep diff --git a/interim/rnaseq_clstr/piper25/transcriptome_clstr.pep.clstr b/interim/cdhit/piper25/transcriptome_clstr.pep.clstr similarity index 100% rename from interim/rnaseq_clstr/piper25/transcriptome_clstr.pep.clstr rename to interim/cdhit/piper25/transcriptome_clstr.pep.clstr diff --git a/interim/rnaseq_clstr/piper26/transcriptome_clstr.pep b/interim/cdhit/piper26/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper26/transcriptome_clstr.pep rename to interim/cdhit/piper26/transcriptome_clstr.pep diff --git a/interim/rnaseq_clstr/piper26/transcriptome_clstr.pep.clstr b/interim/cdhit/piper26/transcriptome_clstr.pep.clstr similarity index 100% rename from interim/rnaseq_clstr/piper26/transcriptome_clstr.pep.clstr rename to interim/cdhit/piper26/transcriptome_clstr.pep.clstr diff --git a/interim/rnaseq_clstr/piper27/transcriptome_clstr.pep b/interim/cdhit/piper27/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper27/transcriptome_clstr.pep rename to interim/cdhit/piper27/transcriptome_clstr.pep diff --git a/interim/rnaseq_clstr/piper27/transcriptome_clstr.pep.clstr b/interim/cdhit/piper27/transcriptome_clstr.pep.clstr similarity index 100% rename from interim/rnaseq_clstr/piper27/transcriptome_clstr.pep.clstr rename to interim/cdhit/piper27/transcriptome_clstr.pep.clstr diff --git a/interim/rnaseq_clstr/piper32/transcriptome_clstr.pep b/interim/cdhit/piper32/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper32/transcriptome_clstr.pep rename to interim/cdhit/piper32/transcriptome_clstr.pep diff --git a/interim/rnaseq_clstr/piper32/transcriptome_clstr.pep.clstr b/interim/cdhit/piper32/transcriptome_clstr.pep.clstr similarity index 100% rename from interim/rnaseq_clstr/piper32/transcriptome_clstr.pep.clstr rename to interim/cdhit/piper32/transcriptome_clstr.pep.clstr diff --git a/interim/rnaseq_clstr/piper54/transcriptome_clstr.pep b/interim/cdhit/piper54/transcriptome_clstr.pep similarity index 100% rename from interim/rnaseq_clstr/piper54/transcriptome_clstr.pep rename to 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