Description

Issues Track: v1.0_issues.bed (hifi.pri.issues.bed)<\p>

Methods

This file contains regions with low coverage from HiFi and ONT platforms.

Reads were aligned with Winnowmap 2.01.

Primary read alignments have been processed with asset commit ver. 0133f268eebf308a1c3eb356b564550526465157, and regions meeting the following criteria are reported in each platform:

  • Less than 7 reads aligned in hifi, 10 reads aligned in ONT
  • Merged when regions are less than 5 kb apart
  • Exclude low coverage at both 3 kb ends of each chromosome due to natural coverage drop
  • Exclude low coverage overlapping rDNA gaps

    Issues track from each platform:

  • hifi.pri.issues.bed
  • ont.pri.len1k_idy85.issues.bed (this file contains regions completely overlapping hifi.pri.issues.bed)

    Clipped regions not associated with low coverage:

  • hifi.pri.clipped.bed
  • ont.pri.len1k_idy85.clipped.bed

    Display Conventions and Configuration

  • Low (Low coverage) or Low_Qual (Low coverage associated with consensus error) : 204,0,0 (red)
  • Low_GA/TC, Low_AT (Low coverage from sequencing bias) : 153,153,255 (light purple)
  • Clipped (Region with excessive read clipping) : 153,153,153 (gray)

    Data access

    https://github.com/marbl/CHM13-issues/v1.0_issues.bed

    Release history

    1. 2021 Apr 28. Internal release
    2. 2021 Feb 23. Internal release

    Contacts

    Credits