Robert Aboukhalil

Exercises from [Shell Novice](https://swcarpentry.github.io/shell-novice/) - [x] Finding Things - [x] Shell Scripts

* https://rnabio.org/module-04-kallisto/0004/02/01/Alignment_Free_Kallisto/ * https://pachterlab.github.io/kallisto/starting

Replace `` with regular Markdown format for links: `[text](url)` and add the `target="_blank"` at build time

URL: https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/BCM_Revio_20240313/HG008-T_PacBio-HiFi-Revio_20240313_106x_GRCh38-GIABv3.bam It seems to be downloading the whole bam file (says Pending in network tab for a few mins):  --- This is...

Useful when a structural variant is much smaller than the size of the assembly contig.

Visualize multiple BAMs/VCFs

1

To support tumor vs. normal comparisons, color reads differently for each BAM, with reads grouped vertically, and the bam file names on the side like in IGV

Look into supporting CNV calls

2

Original: Visualize CNV files in addition to SVs, and also viewing these together