Galaxy |

Find clusters of reads (version 0.5.25)

input:

Produce an alignment file containing evidence for insertions.:

Produce a VCF file describing the insertion that have been found.:

produce a GFF file describing the insertions that have been found.:

Produce a fasta file containing assembled contigs.:

Will you select a transposon reference genome from your history or use a built-in index?:

Built-ins were indexed using default options. See `Indexes` section of help below

Using transposon reference genome:

Select transposon genome from the list

Will you select a genome reference genome from your history or use a built-in index?:

Built-ins were indexed using default options. See `Indexes` section of help below

Using genome reference genome:

Select genome genome from the list

Usage: findcluster [OPTIONS]

  Find clusters of reads that support a TE insertion.

Options:
  --input_path PATH               Find cluster in this BAM file.
  --region TEXT                   Find clusters in this Region (Format is
                                  chrX:2000-1000).
  --max_proper_pair_size INTEGER  Maximum proper pairs size. If not given will
                                  be inferred from the data.
  --output_bam PATH               Write out BAM file with cluster information
                                  to this path. Reads will have an additional
                                  "CD" tag to indicate the cluster number
  --output_gff PATH               Write out GFF file with cluster information
                                  to this path.
  --output_fasta PATH             Write out supporting evidence for clusters
                                  to this path.
  --sample_name TEXT              Sample name to use when writing out clusters
                                  in GFF file. Default is to infer the name
                                  from the input filename.
  --include_duplicates / --no-include_duplicates
                                  Include reads marked as duplicates when
                                  finding clusters.
  --transposon_reference_fasta TEXT
                                  Transposon fasta to align clipped reads to.
                                  Not necessary if BWA index is provided.
  --transposon_bwa_index TEXT     Transposon BWA index to align clipped reads
                                  to
  --genome_reference_fasta TEXT   Genome fasta to align clipped reads to. Not
                                  necessary if BWA index is provided.
  --genome_bwa_index TEXT         Genome BWA index to align clipped reads to
  --threads INTEGER RANGE         Threads to use for cap3 assembly step
  --shm_dir PATH                  Path to shared memory folder
  --version                       Show the version and exit.
  --help                          Show this message and exit.