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CLI Commands Reference

Complete reference for all ScanMLST command-line interface parameters.

Overview

❯ scanmst -h

usage: scanmst [-h] [--version] --input INPUT --ref REF --gtf GTF --output OUTPUT [--output-seq {consensus,reference,both}] [--sr SUPPORT_READS]
               [--splice-bin SPLICE_BIN] [--mapq MAPQ] [--log-level {info,debug,trace,warning}] [--parallel PARALLEL] [--aligner {blat,}]
               [--blat-identity IDENT_CUTOFF] [--blat-2bit BLAT_TWO_BIT] [--blat-nclosed] [--blat-nsleep] [--blat-port BLAT_PORT] [--species {human,mouse}]
               [--circular-rna-filter {remove,keep,extract}] [--off-exon-filter] [--rt-switching-filter RT_SWITCHING_FILTER_LEN] [--ncan] [--graph] [--refine] [--refine-threshold REFINE_THRESHOLD]
               [--nbound] [--max-allowed-nm MAX_ALLOWED_NM] [--max-allowed-ins MAX_ALLOWED_INS] [--min-required-ins MIN_REQUIRED_INS] [--long-indel-length LONG_INDEL_LENGTH]
               [--indel-fraction INDEL_FRACTION] [--prune-threshold PRUNE_THRESHOLD] [--soft-len SOFT_LEN]
               [--mismatch MISMATCH] [--min-soft-seg-len MIN_SOFT_SEG_LEN] [--alignment-fraction ALIGNMENT_FRACTION]
               [--substitution-fraction SUBSTITUTIONS_FRACTION] [--ignore-circle] [--rescue-sr]

scanmst 🚀 Multi-segment transcript (MST) identification using transcriptomic long reads data

options:
  -h, --help                              show this help message and exit
  --version                               show program's version number and exit
  --input INPUT                           Input alignment BAM file, which must contain both cs and SA tags.
  --ref REF                               Reference genome in FASTA format (with fai index)
  --gtf GTF                               Gene annotations in GTF format
  --output OUTPUT                         Output file prefix
  --output-seq {consensus,reference,both}
                                          Output sequence type (default: consensus)
  --sr SUPPORT_READS                      The minimum number of supporting reads required for calling MST. (default: 1)
  --splice-bin SPLICE_BIN                 Bin size for searching canonical splice sites. (default: 5)
  --mapq MAPQ                             Minimum MAPQ of reads required for calling MST. (default: 20)
  --log-level {info,debug,trace,warning}  Set log level (default: warning)
  --thread THREAD                         Set the thread number (default: 1)
  --aligner {blat,}                       Aligner used for additional realignment to recover missing chimeric alignments. (default: None)
  --blat-identity IDENT_CUTOFF            BLAT identity cutoff (default: 0.9)
  --blat-2bit BLAT_TWO_BIT                Reference genome in 2bit format for BLAT aligner
  --blat-nclosed                          Close BLAT server when the job is complete (default: True)
  --blat-nsleep                           Whether to sleep randomly before starting BLAT server (default: True)
  --blat-port BLAT_PORT                   Port for BLAT server (default: 88888)
  --species {human,mouse}                 Name of the species for the reference genome (default: human)
  --circular-rna-filter {remove,keep,extract}
                                          The way of dealing with putative circular RNAs (default: remove)
  --off-exon-filter                       Turn on exon filter (default: True)
  --rt-switching-filter RT_SWITCHING_FILTER_LEN
                                          Set the length threshold for RT switching filter. (default length: 10)
  --ncan                                  Considering non-canonical splice sites (default: False)
  --graph                                 Whether to output transcript segment graph. (default: False)
  --refine                                Whether to refine the transcript segment graph after construction. (default: False)
  --refine-threshold REFINE_THRESHOLD     Threshold for merging nodes during refinement (default: 3)
  --prune-threshold PRUNE_THRESHOLD       Length threshold for pruning the transcript segment graph (default: 10)
  --max-allowed-nm MAX_ALLOWED_NM         Maximum allowed edit distance (NM tag). (default: 100)
  --max-allowed-ins MAX_ALLOWED_INS       Maximum allowed micro-insertion length (default: 50)
  --min-required-ins MIN_REQUIRED_INS     Minimum required insertion length in read to infer chimeric alignment (default: 100)
  --min-soft-seg-len MIN_SOFT_SEG_LEN     Minimum length of soft-clipped portion required to trigger BLAT alignment. (default: 200)
  --long-indel-length LONG_INDEL_LENGTH   Length cutoff for defining long indels in reads. (default: 10)
  --indel-fraction INDEL_FRACTION         Maximum allowed fraction of long indels in the reads. (default: 0.001)
  --substitution-fraction SUBSTITUTIONS_FRACTION
                                          Maximum allowed fraction of substitutions in the reads (default: 0.05)
  --rescue-sr                             Whether to rescue SR for segment links (default: False)
  --soft-len SOFT_LEN                     Minimum length of soft-clipped portion to be rescued (default: 5)
  --mismatch MISMATCH                     Maximum number of mismatched bases allowed in a rescued segment (default: 3)
  --alignment-fraction ALIGNMENT_FRACTION
                                          Minimum fraction of the sequence that must align in Smith-Waterman local alignment. (default: 0.8)
  --nbound                                Whether to add maximum increment limit using average reads depth when rescuing SR (default: True)
  --ignore-circle                         Whether to export result when the transcript segment graph contains a circle (default: False)

--version

Display ScanMST version information.

scanmst --version

Output:

scanmst 0.1.7

--help, -h

Display help information for all commands.

scanmst --help

Essential Arguments

--input

Input the alignment BAM file, which must have cs and SA tags in it.

--ref

Reference genome FASTA file.

--gtf

Gene annotation GTF file

--output

Output file prefix

Optional Arguments

--output-seq

Output sequence type

Default: consensus

  • consensus: consensus sequences derived from reads
  • reference: sequences based on the reference genome
  • both: consensus and reference sequences

--sr

Default: 1

The minimum number of supporting reads (SRs) required to report an MST.

It is defined at the transcript level as the minimum SR across all its segment links, each segment link has a corresponding SR and must meet this minimum threshold.

--splice-bin

Default: 5

Bin size for searching canonical splice sites.

--aligner

Default: None

Option: blat

Aligner used for additional realignment to recover missing chimeric alignments.

--blat-2bit

The reference genome in 2BIT format is required only when the --aligner option is set to blat

--blat-port

Default: 88888

Port for BLAT server.

--circular-rna-filter

Default: remove

The way of dealing with putative circular RNAs.

  • remove: remove putative circular RNAs.
  • keep: keep putative circular RNAs.
  • extract: extract putative circular RNAs only.

--off-exon-filter

Default: True

Disable exon filter. When enabled by default, this filter removes segment links whose both ends fall within the same exon. Setting --off-exon-filter turns this filtering off.

--rt-switching-filter

Default: 10

Set the length threshold for RT switching filter.

--ncan

Default: False

When enabled, segment links involving non-canonical splice sites are included.

--graph

Default: False

Whether to output the graph. When enabled, transcript segment graphs are exported in JSON format.

--refine

Default: False

Whether to refine the transcript segment graph after construction. When enabled, transcript segment graph will be refined.

--refine-threshold

Default: 3

Threshold (in base pairs) for merging nodes during graph refinement. Nodes with the same chromosome, strand, and intron structure whose start and end positions differ by at most this threshold will be merged. Only applies when --refine is enabled.

--max-allowed-nm

Default: 100

Maximum allowed edit distance (NM tag) in the alignment.

--max-allowed-ins

Default: 50

Maximum allowed micro-insertion length.

--min-required-ins

Default: 100

Minimum required insertion length in read to infer chimeric alignment.

--min-soft-seg-len

Default: 200

Minimum length of soft-clipped portion required to trigger BLAT alignment to infer chimeric alignment.

--long-indel-length

Default: 10

Length cutoff for defining long indels in reads.

--indel-fraction

Default: 0.001

Maximum allowed fraction of long indels in the reads

--substitution-fraction

Default: 0.05 Maximum allowed fraction of substitutions in the reads.

--prune-threshold

Default: 10

Length threshold for pruning the transcript segment graph.

--ignore-circle

Default: False

Whether to export result when the transcript segment graph contains a circle.

--rescue-sr

Default: False

Whether to rescue SR for segment links. Disabled by default. When disabled, soft-clipped portions of non-chimeric alignments are not used to increase the SR count.

--soft-len

Default: 5

Minimum length of soft-clipped portion to be rescued.

--mismatch

Default: 5

Maximum number of mismatched bases allowed in a rescued segment

--alignment-fraction

Default: 0.8

Minimum fraction of the sequence that must align in Smith-Waterman local alignment.

--nbound

Default: True

Whether to add maximum increment limit using average reads depth when rescuing SR. Enabled by default.

See Also