changes to chapter 3. Raw data processing #327
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I will still have to change a link in the document! |
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When I build the book locally, “Zappia and Theis, 2021” jumps to the preamble (row 14). I don't have this problem when I build the book with the main. I couldn't find a solution so far! |
Might fix the link problem
Zethson
reviewed
Feb 6, 2025
Co-authored-by: Lukas Heumos <[email protected]>
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…gle-cell-best-practices into feature/raw-data-processing
This reverts commit e9acdfc.
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
Co-authored-by: Lukas Heumos <[email protected]>
…gle-cell-best-practices into feature/raw-data-processing
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changes from @Zethson 's feedbacks have been applied, besides the |
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I fixed the link issue, it was probably because markdown thinks |
Signed-off-by: Lukas Heumos <[email protected]>
Zethson
reviewed
Feb 11, 2025
| adapter sequences | ||
| Short, synthetic DNA or RNA sequences that are ligated to the ends of DNA or RNA fragments during library preparation for sequencing. | ||
| These adapters are essential for binding the fragments to the flowcell and enabling amplification and sequencing. | ||
| However, if adapters are not properly removed or trimmed after sequencing, they can appear in the reads, potentially interfering with alignment and downstream analyses. |
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| However, if adapters are not properly removed or trimmed after sequencing, they can appear in the reads, potentially interfering with alignment and downstream analyses. | |
| However, if adapters are not trimmed after sequencing, they can appear in the reads, potentially interfering with alignment and downstream analyses. |
| MuData | ||
| A Python package for multimodal annotated data matrices. The primary data structure in the scverse ecosystem for multimodal data. | ||
| A Python package for multimodal annotated data matrices. |
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| A Python package for multimodal annotated data matrices. | |
| A Python package for multimodal annotated data matrices that builds on {term}`AnnData`. |
| signal-to-noise ratio | ||
| A measure of the clarity of a signal relative to background noise. | ||
| In sequencing, the signal represents the detectable information derived from the DNA or RNA molecules being sequenced, while the noise includes random errors or unwanted signals that can obscure or distort the true data. | ||
| A high SNR indicates that the signal is strong and reliable compared to the noise, resulting in better data quality. |
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This glossary item didn't introduce the SNR acronym right?
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| Spike-in RNA | ||
| RNA transcripts of known sequence and quantity to calibrate measurements in RNA hybridization steps for RNA-seq. | ||
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| Splice Junctions | ||
| splice junctions | ||
| Locations where introns are removed, and exons are joined together in a mature RNA transcript during RNA splicing. These junctions occur at specific nucleotide sequences and are critical for the proper assembly of functional mRNA. |
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| Locations where introns are removed, and exons are joined together in a mature RNA transcript during RNA splicing. These junctions occur at specific nucleotide sequences and are critical for the proper assembly of functional mRNA. | |
| Locations where introns are removed, and exons are joined together in a mature RNA transcript during RNA splicing. | |
| These junctions occur at specific nucleotide sequences and are critical for the proper assembly of functional mRNA. |
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I cleaned the sentences of chapter 3. Raw data processing.
Please have a look when you have time :)