bowtie demonstration

by rnnh 4 years ago

GNU/Linux ◆ xterm-256color ◆ bash 1598 views

In this video, bowtie-build is used to indexS_cere_GCF_000146045.2_R64_genomic.fna, which is a copy of the Saccharomyces cerevisiae S288C genome from RefSeq. The bowtie command is then used to align Saccharomyces cerevisiae RNAseq reads to this bowtie index.

Made for https://rnnh.github.io/bioinfo-notebook/

More by rnnh

bowtie2 demonstration 02:00

by rnnh 4 years ago

fastq-dump_to_featureCounts.sh demonstration two 16:28

by rnnh 4 years ago

featureCounts demonstration 01:36

by rnnh 4 years ago

wgsim demonstration 01:07

by rnnh 4 years ago

See all

You can download this recording in asciicast v2 format, as a .cast file.

Download

Replay in terminal

You can replay the downloaded recording in your terminal using the asciinema play command:

asciinema play 316272.cast

If you don't have asciinema CLI installed then see installation instructions.

Use with stand-alone player on your website

Download asciinema player from the releases page (you only need .js and .css file), then use it like this:

<!DOCTYPE html>
<html>
<head>
  <link rel="stylesheet" type="text/css" href="asciinema-player.css" />
</head>
<body>
  <div id="player"></div>
  <script src="asciinema-player.min.js"></script>
  <script>
    AsciinemaPlayer.create(
      '/assets/316272.cast',
      document.getElementById('player'),
      { cols: 80, rows: 30 }
    );
  </script>
</body>
</html>

See asciinema player quick-start guide for full usage instructions.

While this site doesn't offer GIF conversion at the moment, you can still do it yourself with the help of asciinema GIF generator utility - agg.

Once you have it installed run the following command to create GIF file:

agg https://asciinema.org/a/316272 316272.gif

Or, if you already downloaded the recording file:

agg 316272.cast 316272.gif

Check agg --help for all available options. You can change font family and size, select color theme, adjust speed and more.

See agg manual for full usage instructions.