bergmanlab/mcclintock

Issues

• Compile papers using McClintock pipeline

  #40 opened 2 years ago by cbergman
  10

• A question of ngs_mapper2 output file abount malformed.bed

  #125 opened 7 months ago by craftor18
  0

• Repeate make annotation run after a preprocessing for --make_annotation

  #124 opened 8 months ago by craftor18
  7

• How to Prepare Consensus Sequences

  #123 opened a year ago by Song-10-YF
  0

• Snakefile is not on where is not suppose to be

  #122 opened a year ago by Tcvalenzuela
  0

• Teflon Postprocessing Failure: Error: malformed BED entry at line 57. Start Coordinate detected that is < 0. Exiting.

  #121 opened a year ago by TobyBaril
  3

• Error in rule repeatmask: can't find Repeatmasker output

  #120 opened a year ago by TobyBaril
  12

• Issue running relocaTE2

  #119 opened a year ago by motto7
  5

• thanks for making this

  #118 opened a year ago by tmcclintock
  1

• Failed to solve conda environment for mcc_relocate2

  #113 opened a year ago by s-andrews
  6

• Read name provided with no suffix in trimgalore.log

  #104 opened 2 years ago by dgodin19
  5

• About the consensus fasta file

  #117 opened 2 years ago by Song-10-YF
  2

• ID problems in taxonomy and locations files

  #64 opened 4 years ago by acontrerasg
  6

• Problem with installing Temp and Relocate

  #110 opened 2 years ago by Psula23
  4

• cannot import name '_aligners' from partially initialized module 'Bio.Align'

  #115 opened 2 years ago by rattei
  8

• Summary output

  #111 opened 2 years ago by ebhmayra
  4

• KeyError: 'ngs_te_mapper2'

  #98 opened 2 years ago by jingydz
  3

• RepeatMasker error

  #107 opened 2 years ago by ebhmayra
  14

• Installation of ngs_te_mapper2 fails

  #92 opened 2 years ago by ValentinaBoP
  7

• java.lang.OutOfMemoryError error prompted by running te-locate

  #93 opened 3 years ago by andreabours
  4

• Error running mcclintock.py with testdata from download_test_data.py

  #97 opened 2 years ago by maxcoenen
  4

• Mcclintock stuck on "prepping read" or "reference fasta created"

  #101 opened 2 years ago by dgodin19
  3

• How to run mcclintock with a bash script?

  #100 opened 2 years ago by dgodin19
  3

• Is there a way to speed up installation?

  #99 opened 2 years ago by dgodin19
  1

• A question about running multi samples

  #96 opened 2 years ago by Morriyaty
  3

• Integration of RelocaTE2 results into the relocate2_nonredundant.bed and summary files appears to be incorrect

  #95 opened 3 years ago by andreabours
  2

• How to install tools manually ?

  #94 opened 3 years ago by Morriyaty
  3

• error after running testing dataset.

  #89 opened 3 years ago by yanhaidong1
  7

• Running on test data fails; trimgalore encountering errors

  #86 opened 3 years ago by sbresnahan
  6

• result files empty or not generated - ngs_te_mapper2 and popoolationTE2

  #84 opened 3 years ago by OctavioSerra
  6

• Error in rule repeatmask

  #88 opened 3 years ago by danicats
  5

• Investigate adding iMGEins

  #55 opened 3 years ago by cbergman
  0

• Failed to solve scheduling problem with ILP solver

  #82 opened 4 years ago by ch8316f5eyu
  3

• Error trying to execute glpsol

  #79 opened 4 years ago by acontrerasg
  4

• Question

  #81 opened 4 years ago by ohan-Bioinfo
  6

• teflon error

  #76 opened 4 years ago by tomaszjacek
  17

• git error (fatal: not a git repository (or any of the parent directories): .git)

  #75 opened 4 years ago by tomaszjacek
  5

• Investigate adding PopoolationTE2

  #53 opened 4 years ago by cbergman
  0

• Miss --make_annotations and --mem arguments

  #69 opened 4 years ago by yanhaidong1
  2

• RelocaTE and RelocaTE2 run infinitely or freeze

  #61 opened 4 years ago by lhemmer
  38

• Genotype or merge TIPs across samples?

  #65 opened 4 years ago by YTLogos
  2

• Random error

  #62 opened 4 years ago by Thatguy027
  4

• The fasta consensus set of TE sequences

  #57 opened 4 years ago by YTLogos
  1

• Refactor branch consistently failing with test data on RelocaTE2

  #54 opened 5 years ago by davidecarlson
  6

• mcclintock.sh Segmentation fault

  #50 opened 5 years ago by mehmetdayi
  11

• No such file or directory

  #49 opened 5 years ago by Caro-Ca
  23

• No such file or directory

  #52 opened 5 years ago by Caro-Ca
  3

• WARNING. chromosome (chrXV) was not found in the FASTA file. Skipping.

  #51 opened 5 years ago by Caro-Ca
  0

• install.sh: 108: install.sh: Syntax error: "(" unexpected (expecting "}")

  #48 opened 5 years ago by Caro-Ca
  11

• RepeatMasker modifies some TE names

  #46 opened 6 years ago by gbdias
  0