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@LaurenceKuhl
LaurenceKuhl committed Mar 20, 2024
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1 change: 1 addition & 0 deletions CITATIONS.md
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Expand Up @@ -43,6 +43,7 @@
> Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal, 17(1), pp. 10-12. doi:https://doi.org/10.14806/ej.17.1.200
- [Samtools](10.1093/bioinformatics/btp352)

> Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. doi: 10.1093/bioinformatics/btp352. Epub 2009 Jun 8. PMID: 19505943; PMCID: PMC2723002.
- [MAGeCKFlute](https://doi.org/10.1038/s41596-018-0113-7)
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4 changes: 2 additions & 2 deletions docs/usage/screening.md
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Expand Up @@ -66,8 +66,8 @@ CRISPRcleanR is used for gene count normalization and the removal of biases for
Most used library already have an annotation dataset which you can find [here](https://github.com/francescojm/CRISPRcleanR/blob/master/Reference_Manual.pdf). To use CRISPRcleanR normalization, use `--crisprcleanr library`, `library` being the exact name as the library in the CRISPRcleanR documentation (e.g: "AVANA_Library").
Otherwise, if you wish to provide your own file, please provide it in csv form, and make sure it follows the following format :

| ,CODE | GENES | EXONE | CHRM | STRAND | STARTpos | ENDpos |
|---------------|-------------|-------------|------|--------|----------|----------|
| ,CODE | GENES | EXONE | CHRM | STRAND | STARTpos | ENDpos |
| -------------------- | ----------- | ------------- | ---- | ------ | -------- | -------- | -------- |
| ATGGTGTCCATTATAGCCAT | NM_021446.2 | 0610007P14Rik | ex2 | 12 | + | 85822165 | 85822185 |
| CTCTACGAGAAGCTCTACAC | NM_021446.2 | 0610007P14Rik | ex2 | 12 | + | 85822108 | 85822128 |
| GACTCTATCACATCACACTG | NM_021446.2 | 0610007P14Rik | ex4 | 12 | + | 85816419 | 85816439 |
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90 changes: 23 additions & 67 deletions modules.json
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