Issues

• Can Trimmomatic be skipped while running Wochenende ?

  MHH-RCUG/Wochenende#223 · Filter by author arpit20328 opened on Sep 3, 2024
  4

• When input cfdna fastq data is masked (human reads are masked)

  MHH-RCUG/Wochenende#222 · Filter by author arpit20328 opened on Aug 30, 2024
  3

• Definition of long and short read in wochenende

  MHH-RCUG/Wochenende#221 · Filter by author arpit20328 opened on Apr 4, 2024
  1

• Not able to find "AlignerBoost.jar" on internet .

  MHH-RCUG/Wochenende#220 · Filter by author arpit20328 opened on Mar 27, 2024
  4

• Not able to find file named "adapters_solid.fa"

  MHH-RCUG/Wochenende#219 · Filter by author arpit20328 opened on Mar 27, 2024
  2

• remove alignerboost code

  MHH-RCUG/Wochenende#212 · Filter by author colindaven opened on Mar 9, 2022
  

• reporting errors

  MHH-RCUG/Wochenende#206 · Filter by author colindaven opened on Jan 24, 2022

• bbsplit attempt

  MHH-RCUG/Wochenende#202 · Filter by author colindaven opened on Dec 6, 2021

• upgrade minimap2

  MHH-RCUG/Wochenende#198 · Filter by author colindaven opened on Nov 19, 2021

• use fastp as about twice as fast as fastqc - test

  MHH-RCUG/Wochenende#196 · Filter by author colindaven opened on Nov 9, 2021

• create optional cleanup script, especially for reporting.

  MHH-RCUG/Wochenende#181 · Filter by author colindaven opened on Sep 29, 2021
  5

• Trial tiebrush instead of mapping quality MQ

  MHH-RCUG/Wochenende#174 · Filter by author colindaven opened on Sep 8, 2021

• NM bamtools curiosity : a few reads slip through

  MHH-RCUG/Wochenende#143 · Filter by author colindaven opened on Jun 25, 2021
  1

• reduce bash scripts to single script with functions

  MHH-RCUG/Wochenende#140 · Filter by author colindaven opened on Jun 24, 2021
  

• tests

  MHH-RCUG/Wochenende#131 · Filter by author colindaven opened on May 25, 2021
  

• postprocess - check dependencies at start before running

  MHH-RCUG/Wochenende#130 · Filter by author colindaven opened on May 21, 2021

• check lambda phage reads in ONT

  MHH-RCUG/Wochenende#98 · Filter by author colindaven opened on Jan 8, 2021

• mapping stats - revise for PE reads

  enhancement
  MHH-RCUG/Wochenende#92 · Filter by author colindaven opened on Nov 13, 2020

• Redesign and revise tests

  MHH-RCUG/Wochenende#91 · Filter by author colindaven opened on Nov 13, 2020
  2

  

• PE reads - unmapped sequences not output

  MHH-RCUG/Wochenende#88 · Filter by author colindaven opened on Nov 6, 2020

• make singularity container

  MHH-RCUG/Wochenende#61 · Filter by author colindaven opened on Jun 9, 2020
  6

  

• request: allow more mismatches (scale by read length)

  MHH-RCUG/Wochenende#60 · Filter by author colindaven opened on May 27, 2020
  3

  

• add long read tests

  MHH-RCUG/Wochenende#41 · Filter by author colindaven opened on Mar 23, 2020
  1