oushujun / TAIR12-TE

A repository to host scripts for annotating TEs in the Arabidopsis TAIR12 (Col-CC) genome

TAIR12-TE

A repository to host scripts for annotating TEs in the Arabidopsis TAIR12 (Col-CC) genome

Merge hits

After obtaining initial annotations using EDTA, a post-processing step was conducted to merge annotated fragments. The pipeline considers all neighboring fragments of the same family within a specific proximity. It then searches for a merged stretch over these fragments, including the regions between fragments, in the reference genomes. If the copy number is high enough (at least 3 additional locations beyond its original position), this stretch is considered as an independent mobile sequence and is introduced into the annotation as a "parent".

The following parameters control the merging process:

• P_SIM: Percentage similarity threshold, set to 80%.
• P_COV: Percentage coverage threshold, set to 95%.
• N_CNT: Minimum number of additional occurrences required, set to 4.
• N_DIST: Maximum distance between fragments, set to 1000.

The pipeline requires the following input files:

1. GFF File: The .gff file containing initial annotations generated by EDTA.

   • Path: data/gff/GCA_028009825.2_Col-CC_genomic.fna.mod.EDTA.TEanno.clean.rename.ORFinfo.soloLTR.ATHILA.ONSEN.Evade.TRASH.update_AGI.rm_overlap.20240925.gff3

2. Genome File: The reference genome in FASTA format.

   • Path: data/genome/GCA_028009825.2_Col-CC_genomic.fasta

3. Output Path: The directory for storing output files from the merging pipeline.

   • Path: data/out_merge/

To execute the merging pipeline, please install pannagram and use the following command:

conda activate pannagram 

P_SIM=80
P_COV=95
N_CNT=4
N_DIST=1000

TYPES="Mutator,LINE,hAT_TIR,DNA_transposon,LTR"

FILE_GFF="data/gff/GCA_028009825.2_Col-CC_genomic.fna.mod.EDTA.TEanno.clean.rename.ORFinfo.soloLTR.ATHILA.ONSEN.Evade.TRASH.update_AGI.rm_overlap.20240925.gff3"
FILE_GENOME="data/genome/GCA_028009825.2_Col-CC_genomic.fasta"

PATH_OUTPUT="data/out_merge/"

./merge_pipeline.sh -i  ${FILE_GFF} \
    -g  ${FILE_GENOME} \
    -o  ${PATH_OUTPUT} \
    -s ${P_SIM} \
    -c ${P_COV} \
    -n ${N_CNT} \
    -d ${N_DIST} \
    -p ${TYPES} \
    -v