# Public MAGeCK/Yusa real-data excerpt

This fixture contains unmodified FASTQ records from two public sequencing runs
used by the official MAGeCK real-data tutorial:

| Included file | ENA run | Biological sample | Source archive |
| --- | --- | --- | --- |
| `FastQ/ERR376998_plasmid.fastq` | ERR376998 | plasmid library | `ERR376998.fastq.gz` |
| `FastQ/ERR376999_ESC.fastq` | ERR376999 | mouse ESC screen | `ERR376999.fastq.gz` |

Source run metadata:

- Study: `PRJEB4038`
- ERR376998 archive:
  `https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR376/ERR376998/ERR376998.fastq.gz`
  (282,339,185 bytes; MD5 `7b552f8efd6fe90fc6bc34879c617040`)
- ERR376999 archive:
  `https://ftp.sra.ebi.ac.uk/vol1/fastq/ERR376/ERR376999/ERR376999.fastq.gz`
  (290,645,388 bytes; MD5 `be96811adce2f5d69efd18a02f8e2416`)
- Tutorial:
  `https://sourceforge.net/p/mageck/wiki/demo/#the-third-tutorial-going-through-a-public-crisprcas9-screening-dataset`

`ReferenceLibrary/Yusa_ERR37699x_excerpt.txt` is a 64-guide subset of the
published Yusa mouse knockout library distributed by MAGeCK:

`https://downloads.sourceforge.net/project/mageck/libraries/yusa_library.csv.zip`

The source ZIP has MD5 `3afc334d8beb247784421b88807b7d0e` and SHA-256
`1c63f55c64751f87301f56ce3cb00cc3b9615b40804f99858f5df3b8ce533f82`.

## Reproducible extraction

The fixture was produced without changing sequence or quality data:

1. Read the first 100,000 complete records from each source FASTQ archive.
2. Take bases 24-42 (the tutorial's 23-base prefix followed by the 19-base
   Yusa guide).
3. Keep guides present in the Yusa library and in both runs.
4. Rank guides by their combined exact-match count in the two excerpts,
   breaking ties lexicographically by guide sequence, and retain the first 64.
5. Retain every original FASTQ record for those 64 guides.

That yields 743 plasmid records and 971 ESC records.
`CountTable/ExpectedCountTable.txt` was calculated directly from the extracted
19-base guide sequence in each retained read. It is the independent expected
answer used by the integration tests; it is not output captured from Library
Aligner.

Because these guides are 19 bases long, run the retained alignment engine with
a 9-base piece size and an 18-base minimum alignment size. The legacy k-mer
loop emits 10 windows for a 19-base guide, so an alignment minimum of 19 would
require one more window than that engine produces.
