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Reform_python.md

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Using Reform to create custom genome

https://gencore.bio.nyu.edu/reform/

  • You can find good example with cellRanger in this link.

Usage guide

Conda env. and install

module load gcc/6.2.0 conda2/4.2.13
conda activate python_3.6.5 # you need an environment with python3 activated. (this one is custom for me)
pip3 install biopython
git clone https://github.com/gencorefacility/reform.git 
cd reform/

The command code and the files we need.

  --chrom=<chrom> \
  --position=<pos> \ 
  --in_fasta=<in_fasta> \
  --in_gff=<in_gff> \
  --ref_fasta=<ref_fasta> \
  --ref_gff=<ref_gff>

  • chrom ID of the chromsome to modify

  • position Position in chromosome at which to insert <in_fasta>. Can use -1 to add to end of chromosome. Note: Either position, or upstream AND downstream sequence must be provided.

  • upstream_fasta Path to Fasta file with upstream sequence. Note: Either position, or upstream AND downstream sequence must be provided.

  • downstream_fasta Path to Fasta file with downstream sequence. Note: Either position, or upstream AND downstream sequence must be provided.

  • in_fasta Path to new sequence to be inserted into reference genome in fasta format.

  • in_gff Path to GFF file describing new fasta sequence to be inserted.

  • ref_fasta Path to reference fasta file.

  • ref_gff Path to reference gff file.

Example:

python3 reform.py 
 --chrom=X \
 --position=3 \
 --in_fasta=in.fa \
 --in_gff=in.gff3 \
 --ref_fasta=ref.fa \
 --ref_gff=ref.gff3

We will put the in.fa sequence in the X chromosome position 3.

Sequence is 10bp, so we expect a new transcript at X:4-13.

in.fa

>input_sequence
TGGAGGATCG

ref.gff

in.gff

reformed.gff