nlabrad/CIMS-Cyanobacterial-ITS-motif-slicer

Issues

• cant save output file when using genbank fetch.

  #34 opened 2 years ago by callmcgovern
  0

• d1d1 is not outputting anything anymore...

  #33 opened 2 years ago by callmcgovern
  1

• quick fix for when using the -t flag

  #32 opened 2 years ago by callmcgovern
  1

• earlier CCTCCTT prevents finding leader/D1

  #25 opened 2 years ago by phycologia
  4

• wrong boxb found with newest code

  #21 opened 2 years ago by phycologia
  9

• BoxB truncated when script uses primary box b algorithm

  #19 opened 2 years ago by callmcgovern
  1

• Changing naming of tRNAs

  #27 opened 2 years ago by callmcgovern
  1

• Change "motif search" to "CIMS"

  #28 opened 2 years ago by callmcgovern
  1

• make length constraint for boxb on the small end

  #23 opened 2 years ago by callmcgovern
  1

• Genbank -g argument not working. Returns "cannot parse this..."

  #16 opened 2 years ago by callmcgovern
  1

• BoxB sequences not found in fischerella spp

  #20 opened 2 years ago by phycologia
  1

• Do double output for Box B when needed.

  #13 opened 2 years ago by callmcgovern
  1

• Set limit to how long BoxB can be

  #17 opened 2 years ago by callmcgovern
  0

• User specified flanking regions would help with accuracy if the user knows what to look for.

  #18 opened 2 years ago by callmcgovern
  0

• GACCT[...]AGGTC elsewhere in the sequence leads to misidentifying D1

  #5 opened 2 years ago by phycologia
  1

• synechococus and cynobium contain unique 16s ending and d1d1 beginning!

  #7 opened 2 years ago by callmcgovern
  8

• can we make the script load dependecies automagically??

  #14 opened 2 years ago by callmcgovern
  0

• Two ending sequences of D1D1

  #4 opened 2 years ago by aimeee05
  6

• complete output wont save into text file if the sequence doesnt contain ITS regions

  #8 opened 2 years ago by callmcgovern
  1

• snowella d1d1 illuminates an issue

  #10 opened 2 years ago by callmcgovern
  1

• New algorithm only returns results for first sequence in fasta file with many seqs

  #11 opened 2 years ago by callmcgovern
  1

• d1d1 length is "1" every time.

  #12 opened 2 years ago by callmcgovern
  1

• BoxB missed when beginning w CAGCAT

  #6 opened 2 years ago by phycologia
  2

• program quit after 1st organism processed

  #3 opened 2 years ago by callmcgovern
  4

• Monolithic file

  #2 opened 2 years ago by nlabrad
  0