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Fix footnotes, preview #31

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merged 4 commits into from
Jun 6, 2024
Merged

Fix footnotes, preview #31

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bddd2e7
shorter preview with a clear thesis
hexylena Jun 6, 2024
53841a0
fix footnotes
hexylena Jun 6, 2024
66099bc
remove trailing spaces
hexylena Jun 6, 2024
11871ec
remove tracking
hexylena Jun 6, 2024
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14 changes: 10 additions & 4 deletions _posts/2024-06-06-switch-to-bam.md
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Expand Up @@ -5,16 +5,20 @@ tags:
- BAM
- uBAM
- FASTQ
- file formats
- file formats
contributors:
- lskatz
- SeanSierra-Patev
- dbtara
reviewers:
- pmenzel
- hexylena
- hexylena
---

uBAM is a strictly better storage format for your sequencing data, and you should switch to it today.

## Background

It has been over 14 years since the formalization of the FASTQ format ({% cite Cock2009 %}),
which describes sequences and their quality scores.
For paired end reads, sequences are encoded in separate files, usually called R1 and R2 [^1].
Expand Down Expand Up @@ -187,5 +191,7 @@ and [Lyve-SET](https://github.com/lskatz/lyve-SET/), they do not natively read u
I wish I could say that I will address this right away, but with all my other responsibilities, it will be further down the road.
Therefore we can say from our own observations and personal experience, there is some work up ahead to get us moved over to uBAM files!

[^1] To maintain focus in this article, I will gloss past interleaved reads.
[^2] One such example of an organization trying to standardize is [here](https://www.genomeweb.com/informatics/will-bioinformatics-professionals-embrace-mpeg-g-data-compression-standard?utm_source=addthis_shares#.XcwmeiO9qjW.twitter).
### Footnotes

[^1]: To maintain focus in this article, I will gloss past interleaved reads.
[^2]: One such example of an organization trying to standardize is [here](https://www.genomeweb.com/informatics/will-bioinformatics-professionals-embrace-mpeg-g-data-compression-standard).