Jitterbug is a bioinformatic software that predicts insertion sites of transposable elements in a sample sequenced by short paired-end reads with respect to an assembled reference.
1) In documentation and article I couldn't find the meaning of negative zygosity. Could this be a bug?
2) In my work I need to compare ~300 genomes by copy number variation of TEs. How I can parse the gff file for this task? How to interpret the many variants of the annotation listed separated by commas?
3) How can I take into account TEs present in the reference but absent in my samples?
I will be extremely grateful for any help! Thank you again for the tool!
Hi!
Thank you for such useful tool! Can you help me with interpreting the results?
This is the one line of my gff3 output:
chr5H jitterbug TE_insertion 443642706 443642794 . . . supporting_fwd_reads=7; supporting_rev_reads=6; cluster_pair_ID=7690; lib=None; Inserted_TE_tags_fwd=RLX_unknown_HvMo_chr_4H-37161, RLG_unknown_HvMo_chr_4H-97079, RLX_unknown_HvMo_chr_2H-166486, RLX_unknown_HvMo_chr_7H-165987, RLX_unknown_HvMo_chr_0-7571, RLX_unknown_HvMo_chr_4H-84096; Inserted_TE_tags_rev=RLX_unknown_HvMo_chr_7H-124479, RLX_unknown_HvMo_chr_5H-52963, RLX_unknown_HvMo_chr_6H-54046, RLG_Sukkula_HvMo_chr_2H-199, RLX_unknown_HvMo_chr_1H-54792, RLG_unknown_HvMo_chr_2H-74651, RLX_unknown_HvMo_chr_7H-42435; fwd_cluster_span=33; rev_cluster_span=61; softclipped_pos=(-1, -1); softclipped_support=0; het_core_reads=-1; zygosity=-1.000
1) In documentation and article I couldn't find the meaning of negative zygosity. Could this be a bug?
2) In my work I need to compare ~300 genomes by copy number variation of TEs. How I can parse the gff file for this task? How to interpret the many variants of the annotation listed separated by commas?
3) How can I take into account TEs present in the reference but absent in my samples?
I will be extremely grateful for any help! Thank you again for the tool!