BIND prediction
Merge gene predictions of B RAKER (braker-final.gff3
) with gene predictions IN ferred D irectly (DI-final.gff3
).
See the scripts used for BIND here .
Note: See the details to generate these two predictions in braker
and DirectInf
.
Input files for BIND
BRAKER prediction: braker-final.gff3
Direct Inference prediction: DI-final.gff3
reference genome fasta file: TAIR10_chr_all.fas
splice junction file: junctions.bed # from DirectInf step
list of input prediction: list_BIND.txt
Consolidate all the transcripts from BRAKER and DirInf, and predict potential protein coding sequence
Make a configure file and prepare transcripts:
You should prepare a
list_BIND.txt
as below to include gtf path (1st column), gtf abbrev (2nd column), stranded-specific or not (3rd column):1braker-final.gff3 br False 2DI-final.gff3 DI False
Then run the script as below:
1./01_runMikado_round1.sh TAIR10_chr_all.fas junctions.bed list_BIND.txt BIND
This will generate BIND_prepared.fasta file that will be used for predicting ORFs in the next step.
Note:
junctions.bed
is the same file generate from DirectInf step.
1./02_runTransDecoder.sh BIND_prepared.fasta
We will use BIND_prepared.fasta.transdecoder.bed in the next step.
Note: Here we only kept complete CDS for next step. You can revise
02_runTransDecoder.sh
to use both incomplete and complete CDS if you need.
1./03_runMikado_round2.sh BIND_prepared.fasta.transdecoder.bed BIND
This will generate:
1mikado.metrics.tsv 2mikado.scores.tsv 3BIND.loci.gff3
Optional: Filter out transcripts with redundant CDS
1./04_rm_redundance.sh BIND.loci.gff3 TAIR10_chr_all.fas
Optional: Filter out transcripts whose predicted proteins mapped to transposon elements
Note: filter.pep.fa
is an output from previous step for removing redundant CDSs. You can also use all protein sequence if you don’t want to remove redundant CDSs.