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Hello
so I am still reading and digging online this issue and am inquiring about ANNOVAR custom made transcription factor binding site for a mouse mm10 genome.
there are a lot of db avail publicly for ready made use with ANNOVAR however, unlike hg19, there are no ready made tfbs database files avail, and thus I need to create it custom.
After aligning the mouse data, I took the align.bam files and used bed tools bamtobed transformation to create a bed file.
Now my question is how do I use this to create a tfbs annotation with ANNOVAR?
do I just use one of these option for annotate_variation.pl command :
rguments to control input and output
--outfile <file> output file prefix
--zerostart input query file uses half-open zero-start coordinate
--dbtype <string> database type
--buildver <string> genome build version (default: hg18 for human)
--gff3dbfile <file> specify the GFF3 DB file used in region-based annotation
--genericdbfile <file> specify the generic DB file used in filter-based annotation
--vcfdbfile <file> specify the DB file in VCF format in filter-based annotation
-bedfile <file> specify a BED file in region-based annota[/B]tion
so I am still reading and digging online this issue and am inquiring about ANNOVAR custom made transcription factor binding site for a mouse mm10 genome.
there are a lot of db avail publicly for ready made use with ANNOVAR however, unlike hg19, there are no ready made tfbs database files avail, and thus I need to create it custom.
After aligning the mouse data, I took the align.bam files and used bed tools bamtobed transformation to create a bed file.
Now my question is how do I use this to create a tfbs annotation with ANNOVAR?
do I just use one of these option for annotate_variation.pl command :
rguments to control input and output
--outfile <file> output file prefix
--zerostart input query file uses half-open zero-start coordinate
--dbtype <string> database type
--buildver <string> genome build version (default: hg18 for human)
--gff3dbfile <file> specify the GFF3 DB file used in region-based annotation
--genericdbfile <file> specify the generic DB file used in filter-based annotation
--vcfdbfile <file> specify the DB file in VCF format in filter-based annotation
-bedfile <file> specify a BED file in region-based annota[/B]tion