Purpose: To easily extract anntation information from Gencode ENSG/ENST IDs (Biotype,RefSeq Name, ENSG, ENST, status)
How to Run:
cat <gencode list.txt> | perl findBiotypeInfo.pl -d "data-type" -g gencode.gtf
data-type:
-biotype describes the type of transcript (psuedogene, protein coding, ncRNA,etc.)
-geneName returns the UCSC REFSEQ gene name
-ENSG returns the ENSG name that corresponds to all transcripts
-ENST resturn the ENST name that corresponds to all trancsripts
-status retuns the status of annotation on transcripts
genecode list.txt
needs to be a list of either ENST or ENSG names (one per line)
gencode_attributes
10th column of a gtf file of gencode attributes, seperating fields by "\t" instead of ";"
Input list needs to consist of only ENSG IDS or ENST IDs.
The gencode_attributes.txt consists of the 10th column of the Gencode_annotations.gtf file which has ';' replaced by a tab "\t"
To create this file, do the following:
perl -nle 'next if $_=~m/\#{2}/; @a=split(/\t/); @b=split(";",$a[8]); $f=$b[0]; $ENSG=~s/gene_id|\"//g; print join("\t",$ENSG, @b)' gencode.v19.annotation.gtf > annotation_attributes.txt
biotype: psuedogene, protein-coding, ncRNA, etc.
geneName: APOE, ABCA1, GAPDH, etc.
ENSG: ENSG00000227232.4
ENST: ENST00000541675.1
status: KNOWN, NOVEL, or PUTATIVE