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Settings

Required Arguments

  • --gtf - Input GTF file containing transcript annotations.
  • --bed - Input BED file with intron coordinates.
  • --bam - Input BAM file or a TXT file containing a list of BAM files with read alignments.

Warning

Only one of the below input options (GTF, BED, or BAM) should be provided.

  • -r, --reference - Reference FASTA genome used in alignment.
  • -i, --bowtie2_index - Path to Bowtie2 index for the reference genome.

Optional Arguments

  • --bt2_k - Minimum number of distinct alignments found by bowtie2 for a junction to be considered spurious. Default: 10.
  • -o - Length of the overhang on either side of the splice junction. Default: 50.
  • -a - Minimum required anchor length in each of the two exons. Default: 7.
  • --min_duplicate_exon_length- Minimum length that a one-anchor alignment shift must meet or exceed to be considered as representing duplicated exons. It is used to differentiate between exon duplications and spurious splice alignments. Default: 27.
  • --min_junc_score - Minimum number of supporting spliced reads required per junction. Default: 1.
  • --trusted_bed - Path to a BED file path with trusted junctions, which will not be removed by EASTR.
  • --verbose - Display additional information during BAM filtering, including the count of total spliced alignments and removed alignments.
  • --removed_alignments_bam - Write removed alignments to a BAM file.
  • -p - Number of parallel processes. Default: 1.

Minimap2 Parameters

  • -A - Matching score. Default: 3.
  • -B - Mismatching penalty. Default: 4.
  • -O - Gap open penalty. Default: [12, 32].
  • -E - Gap extension penalty. Default: [2, 1].
  • -k - K-mer length for alignment. Default: 3.
  • --scoreN - Score of a mismatch involving ambiguous bases. Default: 1.
  • -w - Minimizer window size. Default: 2.
  • -m - Discard chains with chaining score. Default: 25.

Output Options

  • --out_original_junctions - Write original junctions to the output file or directory.
  • --out_removed_junctions - Write removed junctions to the output file or directory; the default output is to the terminal.
  • --out_filtered_bam - Write filtered bams to the output file or directory.
  • --filtered_bam_suffix - Suffix added to the name of the output BAM files. Default: '_EASTR_filtered'.

Other arguments

  • -p - Number of parallel processes. Default: 1.