clemgoub/dnaPipeTE

Issues

• FileNotFoundError: [Errno 2] No such file or directory: '/dnapipete_3/Trinity.fasta.out'

  #50 opened 4 years ago by mkim0327
  7

• Discrepancy between Trinity.fasta and Reads_per_component_and_annotation output

  #87 opened 4 months ago by emiya52
  1

• PERL Encode error when running DNApipeTE in Singularity

  #86 opened 10 months ago by estolle
  2

• Problem at RepeatMasker stage

  #85 opened a year ago by PatrickCKennedy
  2

• If works with long reads?

  #84 opened a year ago by CWYuan08
  1

• Error in (function (file = if (onefile) "Rplots.pdf" else "Rplot%03d.pdf", : cannot open file 'Rplots.pdf'

  #83 opened a year ago by xx0811
  1

• FATAL message when attempting to rerun program

  #82 opened a year ago by AntonioBaeza
  2

• Inchworm process fails

  #81 opened 2 years ago by sergiogonmoll
  4

• python3: can't open file 'dnaPipeTE.py': [Errno 2] No such file or directory

  #78 opened 2 years ago by AntonioBaeza
  6

• Trinity input not being created?

  #80 opened 2 years ago by nickmiller-iit
  3

• ERROR:main:Error reading file: This file cannot be read by this version of famdb.py.

  #79 opened 2 years ago by AntonioBaeza
  10

• ERROR : Failed to mount squashfs image in (read only): Invalid argument

  #77 opened 2 years ago by AntonioBaeza
  1

• Could i use dnaPipeTE to annotate TE in small Eukaryotic genome ?

  #76 opened 2 years ago by BenAawf
  1

• Any chance to make it available via conda installation?

  #75 opened 2 years ago by AntonioBaeza
  4

• one_RM_hit_per_Trinity_contigs

  #74 opened 2 years ago by GuyBenzvi
  1

• dnaPipeTE.sif

  #67 opened 2 years ago by lablancoberdugo
  6

• Trinity iteration issues with Singularity container

  #66 opened 2 years ago by heidihyang
  4

• Singularity issue

  #65 opened 2 years ago by cahende
  14

• dnaPipeTE vs RepeatModeler

  #59 opened 2 years ago by r-mashoodh
  3

• Repeat Landscape Plots Not Generated

  #58 opened 2 years ago by heidihyang
  6

• TE copies for fully assembled repeats

  #51 opened 2 years ago by zhaolina0827
  8

• RepeatMasker libraries not found

  #46 opened 2 years ago by caroliog
  15

• Installation issue in Linux Redhat 6.2

  #45 opened 2 years ago by nishmadahal
  2

• About input file

  #43 opened 2 years ago by zhang144999
  1

• Problem with repeatmasker modules

  #42 opened 2 years ago by jcerca
  1

• missing 'reads_per_component_and_annotation' in output folder

  #40 opened 2 years ago by avahaley
  1

• forward vs reverse input file?

  #60 opened 2 years ago by r-mashoodh
  3

• Unique TE insertions

  #64 opened 2 years ago by DR-genomics
  1

• FileNotFoundError: [Errno 2]

  #69 opened 2 years ago by lablancoberdugo
  12

• remove int.reads_vs_annoted.blast.out and repeat formatted libraries

  #73 opened 2 years ago by mason-linscott
  1

• Error with Trinity iterations

  #70 opened 2 years ago by filonico
  5

• Question on sampling step

  #72 opened 2 years ago by sigau
  3

• dnaPT_landscapes.sh running error

  #71 opened 2 years ago by Liuxuanzeng
  1

• Update RepeatMasker libraries with RepBase

  #68 opened 3 years ago by sigau
  3

• Error: Issue with producing output graphs

  #63 opened 3 years ago by DR-genomics
  5

• Combining dnaPipeTE and DeepTE outputs

  #62 opened 3 years ago by heidihyang
  3

• Rebuilding TE landscape

  #61 opened 3 years ago by Chloisf
  1

• Figuring out read_per_component_and_annotation/bar_graph and Count.txt

  #37 opened 3 years ago by aryakumar563
  1

• Consolidating output from multiple runs

  #54 opened 3 years ago by andreaswallberg
  1

• dnaPipeTE Runtime/Arguments

  #57 opened 3 years ago by heidihyang
  3

• Cannot remove 'int.reads_vs_annoted.blast.out' file

  #55 opened 3 years ago by pauram
  0

• Trinity.fasta is empty

  #52 opened 4 years ago by buendiad
  3

• others and na classes in Counts.txt output

  #53 opened 4 years ago by ncnlll
  1

• Re-running analysis

  #48 opened 4 years ago by mylena-s
  4

• trinity install as part of dnapipeTE

  #49 opened 4 years ago by signor-molevol
  3

• Installation issue: blastx & makeblastdb not found

  #47 opened 4 years ago by Anh-Thu-Weber
  8

• TE consensus sequences

  #41 opened 4 years ago by zhaolina0827
  5

• Question on input

  #44 opened 4 years ago by jcerca
  3

• Help with paired reads

  #39 opened 4 years ago by bbista
  1

• RepeatMasker checkpoint never triggers as RepeatMasker done

  #38 opened 5 years ago by BagiM
  1