Working with other speciesΒΆ

pyTEnrich has been developed to be used with hg19 genome. If you wish to use it with another genome, you will have to prepare the input TE database with a proper format and make new associated summaries with provided perl script.

Exemple for species danRer10 :

  1. Download TE database from RepeatMasker

2. Convert .fa.out file with utils/convert_repeatMasker.sh utils/convert_repeatMasker.sh danRer10.fa.out > db/danRer10.bed

3. Remove unwanted repeats : grep -v 'Low_complexity\|Satellite\|Simple_repeat\|Unknown' db/danRer10.bed > db/danRer10_TEs.bed

  1. Use utils/make_ref_TE.pl to make files needed by pyTEnrich

    INDEX is the col number of the desired feature (subfam/fam)

class/families should always be in field 6 (0-based) utils/make_ref_TE.pl --file db/danRer10_TEs.bed --index 6 > db/danRer10_Fam_ref_TE.txt

subfam should always be in field 7 (0-based) utils/make_ref_TE.pl --file db/danRer10_TEs.bed --index 7 > db/danRer10_Subfam_ref_TE.txt