MASSeq

RemoveMasSeqTruncatedReads

description
Removes reads that are truncated by the MAS-SEQ adapter.

Inputs

Required

  • bam (File, required): The BAM file to remove truncated reads from.

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • prefix (String, default="out"): The prefix to use for the output BAM file.

Outputs

  • non_trucated_bam (File)
  • non_trucated_bai (File)

AdjustUmiSequenceWithAdapterAlignment

description
Extracts a new UMI from each given read by aligning the preceding adapter sequences to the read.
author
Jonn Smith
email
jonn@broadinstitute.org

Inputs

Required

  • bam (File, required): The BAM file to extract UMIs from.

Optional

  • post_umi_seq (String?): The sequence of the adapter following the UMI sequence.
  • post_umi_tag (String?): The tag to use for the adapter following the UMI sequence.
  • pre_pre_umi_seq (String?): The sequence of the adapter preceding the UMI sequence.
  • pre_umi_seq (String?): The sequence of the adapter preceding the UMI sequence.
  • pre_umi_tag (String?): The tag to use for the adapter preceding the UMI sequence.
  • runtime_attr_override (RuntimeAttr?)

Defaults

  • existing_umi_tag (String, default="ZU"): The tag to use for the existing UMI sequence.
  • new_umi_tag (String, default="JX"): The tag to use for the new UMI sequence.
  • prefix (String, default="out"): The prefix to use for the output BAM file.
  • umi_length (Int, default=10): The length of the UMI sequence.

Outputs

  • umi_adjusted_bam (File)
  • log (File)

FilterMasSeqReads

description
Filters out reads that are likely to be from the MAS-Seq protocol.

Inputs

Required

  • input_bai (File, required): The BAI file for the BAM file to filter.
  • input_bam (File, required): The BAM file to filter.

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • maxEndClipping (Int, default=1000): The maximum amount of end clipping to allow.
  • maxReadLength (Int, default=15000): The maximum read length to allow.
  • prefix (String, default="out"): The prefix to use for the output BAM file.

Outputs

  • bam (File)
  • bai (File)

RenameSingleCellBamTagsForMasIsoSeqV0

description
Rename the single-cell tags in MAS-ISO-seq v0 data (CB -> Jp; ZU -> Jq ...).
author
Jonn Smith
email
jonn@broadinstitute.org

Inputs

Required

  • bam (File, required): The BAM file to rename.

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • prefix (String, default="tags_renamed"): The prefix to use for the output BAM file.

Outputs

  • bam_out (File)
  • bai (File)

RestoreSingleCellBamTagsForMasIsoSeqV0

description
Restore the single-cell tags in MAS-ISO-seq v0 data (Jp -> Cb; Jq -> ZU ...).
author
Jonn Smith
email
jonn@broadinstitute.org

Inputs

Required

  • bam (File, required): The BAM file to rename.

Optional

  • runtime_attr_override (RuntimeAttr?)

Defaults

  • prefix (String, default="tags_restored"): The prefix to use for the output BAM file.

Outputs

  • bam_out (File)
  • bai (File)