ggbio plot with transcripts track and coverage track
1 2 3 4 5 6 7 | plotCoverageOverLocus(
bamfile_path,
annote_db,
gene_id,
strandedness,
quality_threshold = 20L
)
|
bamfile_path |
path to a bam file |
annote_db |
a GenomicFeatures TxDb object. Maybe one made from a gtf, eg txdb = makeTxDbFromGFF("data/liftoff_h99_to_kn99.gtf", format = "gtf") |
gene_id |
a gene_id of interest – must be in the gene names of the annote_db object |
strandedness |
one of c("reverse", "unstranded"). NOTE: forward only strand NOT currently configured |
quality_threshold |
quality threshold above which reads will be considered. 20l is default, which is chosen b/c it is the default for HTSeq |
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