Question regarding the input data for ANEVA-DOT

[lyj95618]

Hello,

I have a question about the input data for ANEVA-DOT. I obtained the ASE result from GATK ASEReadCounter and would like to use ANEVA-DOT for downstream analysis. I looked into the sample_ASE data you shown and noticed that the data format is a bit different from the ASE output from GATK ASEReadCounter. I am wondering how I should deal with the situation that multiple het-SNPs are mapped in a gene, because I don’t see duplicated geneID in the sample_ASE data. Do I sum up all the REF counts and ALT counts for the gene? Or I should pick counts from one of the SNPs?

Thanks in advance.

[geocarvalho]

I don't know if you could proceed with your analysis, but here is what I had to do to see some results:

• Add GENE_ID, based on Ensemble nomenclature, for that use @wickdChromosome variant_level_gene_annotation.
  I followed bw2 recommendation to create a updated gencode file.

git clone https://github.com/wickdChromosome/variant_level_gene_annotation.git
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz
python3 -m pip install pyparsing==2.4.7   # to work around an incompatibility between gtftk and the current version of pyparsing


git clone --branch v1.6.2 --depth 1 https://github.com/dputhier/pygtftk.git
cd pygtftk
# Check your Python version (>=3.8,<3.9)
pip install -r requirements.txt
python setup.py install

wget https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools-2.31.0.tar.gz
tar -zxvf bedtools-2.31.0.tar.gz
cd bedtools2
make

ln -s ${path_to}/bedtools2/bin/bedtools ${path_to}/bin/bedtools

gzcat gencode.v43.annotation.gtf.gz  | gtftk convert -f bed -n feature,gene_id | grep 'gene' | sed 's/gene|//' | awk -v $'OFS=\t' '{ split($4, a, /[.]/); print($1, $2, $3, a[1], $5, $6) }' > gencode.v43.annotation.genes.bed

• Using the script created by @wickdChromosome variant_level_gene_annotation, I just had to adjust cat ${outname}.temp | cut -f-14,18 >> ${outname} inside the bash script to leave the ensemble name in my file.

bash annotate.sh Sample.ASEReadCounter.table gencode.v43.annotation.genes.bed Sample.ASEReadCounter.annotated.table

• Now you have the file that can be used on ANEVA-DOT