https://github.com/samuell/awesome-bioinformatics-gotchas

Gotchas from the trenches of bioinformatics
https://github.com/samuell/awesome-bioinformatics-gotchas

List: awesome-bioinformatics-gotchas

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Gotchas from the trenches of bioinformatics

• Host: GitHub
• URL: https://github.com/samuell/awesome-bioinformatics-gotchas
• Owner: samuell
• License: cc0-1.0
• Created: 2024-12-20T09:52:03.000Z (14 days ago)
• Default Branch: main
• Last Pushed: 2024-12-20T09:52:58.000Z (14 days ago)
• Last Synced: 2024-12-20T10:40:43.027Z (14 days ago)
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• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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# (Not so) Awesome Bioinformatics Gotchas

### Confusing meaning of M operation in CIGAR strings

Wikipedia [writes this](https://en.wikipedia.org/w/index.php?title=Sequence_alignment&oldid=1260199287#CIGAR_Format) about the CIGAR string:

> The original CIGAR format from the [exonerate alignment

> program](https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate)

> did not distinguish between mismatches or matches with the M character.

> 

> The [SAMv1 spec document](https://github.com/samtools/hts-specs/blob/master/SAMv1.pdf) defines newer CIGAR codes. In most cases it is

> preferred to use the `=` and `X` characters to denote matches or mismatches

> rather than the older `M` character, which is ambiguous.

### Count reads is a FASTQ using lines that start with `@`

FASTQ files use `@` to denote the start of a new read, but `@` is also a valid quality score! 

Let's pretend this is your FASTQ:

```

@read_1

ANCACCAGCACGCCGCTGGCCTCCAGCACCAGCTCGCTGGTCAGGCGCAGGCCCGCCTGTTTATCCTCCGCCGTTACCGTCAGGGTGTGTCCCTGCTGCTGCACGTCTGTAGTGGTAAAGACGGGGGAACCGTCCAGCCCCTGGCGATGT

+

@#IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII

@read_2

GCCCGAATCGCAGCAGCAACGCTGCAACCGGTAGCACGGCGATAGGGAGCTGCAAAGCCCTACCGAGGCGCTGGAAAAAACCTAAAATATTCATCCTATTCCCCCTACGAGAACCATTGTTAAGACTCGCGCATAAACTATGTTTTTATC

+

9III999II9I99II9IIII9I99--III-9I-9II-II9I-I-I---IIIIII9999I-II-I-9II9-I--9I9-I---9--9999-9-9999-9I-II9III99999II--I-II-9I-I--IIII999-9-III-9I9-III999-

```

So, you can't simply use something like the following:

```

grep -c "^@" test.fastq

```

Because in `read_1` the quality line begins with `@`, so you will incorrectly get 3 reads, instead of 2.