cultivarium/MicrobeMod

Issues

• Identification of motifs fails with lower-case fasta reference sequences

  #29 opened 7 months ago by tfwulff
  1

• help with troubleshooting the error

  #27 opened 9 months ago by yklight1
  2

• TypeError: can only concatenate str (not "NoneType") to str

  #22 opened 9 months ago by jbeckle3
  9

• Set output directory

  #24 opened 9 months ago by samuelmontgomery
  1

• Reference genomes no longer available

  #25 opened 10 months ago by MarkusHaak
  1

• Matching prodigal call with methylation location

  #17 opened a year ago by Ge0rges
  1

• --percent_cutoff_streme parameter changes _methylated_sites.tsv output

  #23 opened a year ago by winterlich
  3

• Problem with mapped methylated sites

  #19 opened a year ago by MarioRinBarr
  5

• strain comparison

  #21 opened a year ago by stevebaeyen
  1

• All motif locations

  #18 opened a year ago by patrickwest
  1

• Significance of identified motifs?

  #20 opened a year ago by starkeynight
  2

• Feature request: support for 4mC motifs with new models

  #13 opened a year ago by alexweisberg
  7

• 66% threshold rationale

  #3 opened a year ago by Ge0rges
  4

• MAGs

  #16 opened a year ago by Thexiyang
  1

• Support for 4khz Nanopore data

  #15 opened a year ago by 09herbej
  2

• support for previously annotated genome in annotate_rm

  #5 opened a year ago by alexweisberg
  3

• tags/release

  #6 opened a year ago by jowodo
  3

• Step 2 requires SamTools>=1.11?

  #9 opened a year ago by aforestsomewhere
  1

• Permissions on s3 example files?

  #12 opened a year ago by JamesRH
  3

• Conda package

  #2 opened a year ago by Ge0rges
  8

• Unclear why motif is excluded

  #11 opened a year ago by alexweisberg
  4

• pytest fails in /tmp/...

  #7 opened a year ago by jowodo
  4

• HMM gene coverage

  #4 opened a year ago by Ge0rges
  1