Postprocessing_Tasks
CreateCountMatrixFromAnnotatedBam
- description
- Creates a count matrix TSV file from the given annotated bam file. Bam file must contain tags that indicate the gene/transcript (XG), cell barcode (CB), and umi (BX) of the read.
- author
- Jonn Smith
- jonn@broadinstitute.org
Inputs
Required
annotated_transcriptome_bam(File, required): Annotated transcriptome bam file. Must contain tags that indicate the gene/transcript (XG), cell barcode (CB), and umi (BX) of the read.
Optional
runtime_attr_override(RuntimeAttr?)tx_equivalence_class_assignments(File?): Optional file containing a list of equivalence classes for each transcript.
Defaults
prefix(String, default="umi_tools_group"): Prefix for the output file. The output file will be named.tsv umi_tag(String, default="ZU"): The tag that contains the umi. Default is ZU.
Outputs
count_matrix(File)
CreateCountMatrixAnndataFromEquivalenceClasses
- description
- Creates a python anndata object from the given countmatrix tsv and equivalence classes. Expects the input to have been generated by CreateCountMatrixFromAnnotatedBam. The resulting anndata object can be directly read into scanpy for single-cell analysis.
- author
- Jonn Smith
- jonn@broadinstitute.org
Inputs
Required
count_matrix_tsv(File, required): The TSV file containing the count matrix to convert to anndata.gene_equivalence_class_assignments(File, required): The equivalence class assignments file to use for the anndata object.gene_equivalence_class_definitions(File, required): The equivalence class definitions file to use for the anndata object.genome_annotation_gtf_file(File, required): The GTF file containing the genome annotation.tx_equivalence_class_assignments(File, required): The equivalence class assignments file to use for the anndata object.tx_equivalence_class_definitions(File, required): The equivalence class definitions file to use for the anndata object.
Optional
gencode_reference_gtf_file(File?): The gencode reference GTF fileoverlap_interval_label(String?): The label to use for the overlap intervals.overlap_intervals(File?): Overlaping interval file.runtime_attr_override(RuntimeAttr?)
Defaults
force_anndata_gencode_overwrite(Boolean, default=false)prefix(String, default="umi_tools_group"): The prefix to use for the output anndata object.
Outputs
transcript_gene_count_anndata_h5ad(File)pickles(Array[File])
QuantifyGffComparison
- description
- Create equivalence classes and gene assignments from a set of gffcompare results.
- author
- Jonn Smith
- jonn@broadinstitute.org
Inputs
Required
gencode_read_refmap(File, required): Refmap file (produced by gffcompare) comparing the genome reference gtf to input reads (in GFF format).gencode_read_tmap(File, required): Tmap file (produced by gffcompare) comparing the genome reference gtf to input reads (in GFF format).gencode_st2_refmap(File, required): Refmap file (produced by gffcompare) comparing the genome reference gtf to the stringtie2 discovered transcriptome.gencode_st2_tmap(File, required): Tmap file (produced by gffcompare) comparing the genome reference gtf to the stringtie2 discovered transcriptome.genome_gtf(File, required): Genome annotation GTF file (usually gencode).st2_gencode_refmap(File, required): Refmap file (produced by gffcompare) comparing the stringtie2 discovered transcriptome to the genome reference gtf.st2_gencode_tmap(File, required): Tmap file (produced by gffcompare) comparing the stringtie2 discovered transcriptome to the genome reference gtf.st2_read_refmap(File, required): Refmap file (produced by gffcompare) comparing the stringtie2 discovered transcriptome to input reads (in GFF format).st2_read_tmap(File, required): Tmap file (produced by gffcompare) comparing the stringtie2 discovered transcriptome to input reads (in GFF format).
Optional
runtime_attr_override(RuntimeAttr?)
Defaults
prefix(String, default="reads_comparison"): Prefix for ouput file.
Outputs
gene_eq_class_labels_file(File)gene_assignments_file(File)tx_equivalence_class_labels_file(File)tx_equivalence_class_file(File)graph_gpickle(File)
CombineEqClassFiles
- description
- Combine equivalence classes and gene assignments from disjoint sets of reads produced by QuantifyGffComparison.
- author
- Jonn Smith
- jonn@broadinstitute.org
Inputs
Required
equivalence_class_definitions(Array[File], required): TSV files containing transcript equivalence class definitions as produced by QuantifyGffComparison.tx_equivalence_class_labels_file.equivalence_classes(Array[File], required): TSV files containing read -> transcript equivalence class assignments as produced by QuantifyGffComparison.tx_equivalence_class_file.gene_assignment_files(Array[File], required): TSV files containing read -> gene equivalence class assignments as produced by QuantifyGffComparison.gene_assignments_file.gene_eq_class_definitions(Array[File], required): TSV files containing equivalence class definitions for genes as produced by QuantifyGffComparison.gene_eq_class_labels_file.
Optional
runtime_attr_override(RuntimeAttr?)
Defaults
prefix(String, default="combined"): Prefix for ouput file.
Outputs
combined_gene_eq_class_defs(File)combined_gene_eq_class_assignments(File)combined_tx_eq_class_defs(File)combined_tx_eq_class_assignments(File)
CopyEqClassInfoToTag
- description
- Copy the gene assignment for each given read into the given tag for each read.
- author
- Jonn Smith
- jonn@broadinstitute.org
Inputs
Required
bam(File, required): BAM file containing reads to copy gene assignments into.eq_class_file(File, required): TSV file containing read -> gene equivalence class assignments as produced by QuantifyGffComparison.gene_assignments_file.
Optional
runtime_attr_override(RuntimeAttr?)
Defaults
eq_class_tag(String, default="eq"): Tag to copy gene equivalence class into.gene_tag(String, default="XG"): Tag to copy gene assignment into.prefix(String, default="combined"): Prefix for ouput file.
Outputs
bam_out(File)bai(File)