Santhilal Subhash decodebiology

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Decoding Disease Through Data. Advancing Precision Medicine. We combine AI, computational genomics, single-cell multiomics, and regulatory biology.

decodebiology / sample.GTF

Created May 5, 2015 08:32

Sample GTF file

	chr1 processed_transcript exon 11869 12227 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "1"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00002234944";
	chr1 processed_transcript exon 12613 12721 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "2"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00003582793";
	chr1 processed_transcript exon 13221 14409 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "3"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00002312635";
	chr1 transcribed_unprocessed_pseudogene exon 11872 12227 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000515242"; exon_number "1"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-201"; exon_id "ENSE00002234632";
	chr1 transcribed_unprocessed_pseudogene exon 12613 12721 . + . gene_id "ENSG000002

decodebiology / EnsemblGTFtoAnnotation.sh

Last active June 29, 2018 12:18

Convert EnsEMBL GTF to Annotation table (Geneid, GeneSymbol, GeneWiseChrLocation, GeneClass, Strand)

	echo `date`;
	dir=(`dirname $1`)

	base=(`basename $1`)



	echo "1/7 Preparing files";
	cat $1 \| sed 's/ "/\t/g' \| sed 's/"; /\t/g' \| cut -f1,4,5,7,10,12,16,18,22 \| sed 's/";//' \| awk '!x[$6]++' \| awk '{print $6"\t"$0;}' > $dir/enst_annotation.tmp;

decodebiology / baplot.R

Last active August 29, 2015 14:17 — forked from jmmateoshggm/baplot.R