parklab/xTea

Issues

• ImportError: cannot import name 'CascadeForestClassifier' from 'deepforest'

  #129 opened 2 months ago by GianlucaMattei
  12

• Can I run xTEA for mice genomes? & how can i do it?

  #128 opened 3 months ago by sahuno
  3

• ghost_reads.fa.separate_flanking.fa': No such file or directory

  #127 opened 4 months ago by ucsfpan
  0

• Does xtea only detect some subfamilies of TEs in hg38/19?

  #125 opened 4 months ago by sidi-yang
  1

• Dockerfile: RUN rm -rf xTea

  #126 opened 4 months ago by minw2828
  3

• ERROR: No matching distribution found for deep-forest

  #124 opened 5 months ago by minw2828
  1

• About "all_ins_seqs.fa" not found

  #123 opened 5 months ago by 120L021101
  0

• xTea for assembled genomes

  #121 opened 5 months ago by BrendaLee1
  1

• How to extract insertion sequences in short read mode?

  #122 opened 5 months ago by sidi-yang
  1

• Cannot find the target directory: xTea/xtea/genotyping/trained_model_ssc_py2_random_forest_two_category.pkl.

  #120 opened 6 months ago by caroolcardooso-uwa
  3

• Issue with Somatic Insertion Genotyping in Case-Control Mode

  #118 opened 6 months ago by MuratcanMentes
  3

• what's the meaning of "REF_REP=Fall_in_Alu_copy_2.5"?

  #119 opened 6 months ago by sidi-yang
  1

• x_TEA_main.py: error: no such option: --bamsnap

  #100 opened 10 months ago by sidi-yang
  2

• Input file for pseudogene insertion calling

  #116 opened 6 months ago by selee222
  1

• About the case-control analysis in Illumina Short-read WGS Data

  #108 opened 8 months ago by recepyilmaz01
  3

• output vcf

  #77 opened 2 years ago by Sun-Wu-Kong-666
  2

• Will the coverage of BAM files affect the xTea results?

  #110 opened 7 months ago by sidi-yang
  3

• filtering

  #109 opened 7 months ago by jasmineja
  4

• xTea output file understanding

  #107 opened 8 months ago by hhysun
  5

• Possible to merge TE sites and do genotyping in each sample?

  #104 opened 8 months ago by dr-ashu-geno
  1

• long read support with chm13

  #88 opened 8 months ago by maxfieldk
  3

• xTea_long getting stuck, no errors, during wtpoa-cns, running HG38

  #106 opened 9 months ago by vaksmaz
  2

• Alu output didn't go through filter step?

  #105 opened 9 months ago by sidi-yang
  2

• temp files burst out

  #103 opened 9 months ago by sidi-yang
  2

• Long_reads: File detailing which reads show transductions of deletions

  #102 opened 9 months ago by vaksmaz
  1

• line 1133, IOError: [Errno 2] No such file or directory: 'null'

  #99 opened 10 months ago by sidi-yang
  1

• Very long length of L1 insertion

  #101 opened 10 months ago by sidi-yang
  1

• output question

  #75 opened 10 months ago by ohan-Bioinfo
  12

• WES issues

  #94 opened 10 months ago by Nurpe
  1

• xTea Long_read SyntaxWarning

  #98 opened 10 months ago by vaksmaz
  6

• Long read cannot find temp files

  #96 opened 10 months ago by Shezara7
  1

• no such option: --bamsnap

  #84 opened 2 years ago by hzlnutspread
  7

• interpretation of GENE_INFO in output file

  #95 opened a year ago by dongjuleem
  1

• Sporadic inconsistent errors with xtea_long

  #93 opened a year ago by yuliamostovoy
  5

• Merge clip and disc step error

  #92 opened a year ago by Shezara7
  12

• visual inspection using IGV

  #91 opened a year ago by dongjuleem
  0

• Questions about the output file

  #90 opened a year ago by zshu-alt
  3

• Using the code in github still doesn't solve the problem

  #89 opened 2 years ago by zshu-alt
  2

• -f: steps to run. (5907 means run all the steps);

  #87 opened 2 years ago by axz91
  1

• default slurm script with wrong email

  #86 opened 2 years ago by axz91
  1

• HERV doesn't generate .vcf and gets error while reading reads_fa folder

  #82 opened 2 years ago by eduymaz
  1

• Pre-generated Alu database

  #85 opened 2 years ago by drtconway
  1

• Cannot find the target directory

  #83 opened 2 years ago by zshu-alt
  2

• Issue running locally

  #81 opened 2 years ago by RSWilson1
  1

• Handling duplicates

  #80 opened 2 years ago by mikecuoco
  2

• Mosaic calling - missing parameter?

  #78 opened 2 years ago by mukamel-lab
  2

• no enough disc support!

  #79 opened 2 years ago by ohan-Bioinfo
  1

• sklearn version?

  #76 opened 2 years ago by mukamel-lab
  1

• DeprecationWarning

  #73 opened 2 years ago by ohan-Bioinfo
  0

• Gene list Error

  #74 opened 2 years ago by ohan-Bioinfo
  10