... If you have enough RAM and are OK with Python:
from matplotlib import pyplot as plt
sizes = [len(i) for i in pybedtools.BedTool('my.bed')]
... The `gffutils` python package can help with this: https://daler.github.io/gffutils
It will infer the gene and transcript extents; doing so is the default behavior for GTF files. The following will import the GTF into a sqlite3 database (which you can use for other things if needed) and then output ...
... We have an opening for a post-baccalaureate bioinformatics trainee in the Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases at the National Institutes of Health in Bethesda, MD. This is a one year appointment, starting as soon as May 2 ...
written 19 months ago by
Ryan Dale ♦ 4.7k
19 months ago by
Sinji • 2.7k
... Map them both to a reference; the RNA-seq library will be more likely to have splice junctions (look for "N" in the BAM cigar string) and will be sparse in intergenic regions, while the ChIP-seq will have more even coverage, less dynamic range, and will probably have some low-level signal in most pl ...