diff --git a/docs/usage.md b/docs/usage.md index 00cac88b2..296f87da5 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -247,13 +247,13 @@ The `--umitools_grouping_method` parameter affects [how similar, but non-identic #### Examples: -| UMI type | Source | Pipeline parameters | -| ------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf) | `--with_umi --skip_umi_extract --umitools_umi_separator ":"` | -| In sequence | [Lexogen QuantSeq® 3’ mRNA-Seq V2 FWD](https://www.lexogen.com/quantseq-3mrna-sequencing) + [UMI Second Strand Synthesis Module](https://faqs.lexogen.com/faq/how-can-i-add-umis-to-my-quantseq-libraries) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P.{6})(?P.{4}).*"` | -| In sequence | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)
> _mind [Appendix H](https://www.lexogen.com/wp-content/uploads/2020/04/095UG190V0130_CORALL-Total-RNA-Seq_2020-03-31.pdf) regarding optional trimming_ | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P.{12}).*"`
Optional: `--clip_r2 9 --three_prime_clip_r2 12` | -| In sequence | [Takara Bio SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114949.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P.{8})(?P.{6}).*"` | -| In sequence | [Watchmaker mRNA Library Prep Kit](https://watchmakergenomics.com/wp-content/uploads/2023/11/M223_mRNA-Library-Prep-Kit-_UG_WMUG214_v1-1-0823.pdf) with [Twist UMI Adapter System](https://www.twistbioscience.com/sites/default/files/resources/2023-03/DOC-001337_TechNote-ProcessingSequencingDataUtilizingUMI-REV1-singles.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P.{5})(?P.{2}).*" --umitools_bc_pattern2 "^(?P.{5})(?P.{2}).*"` | +| UMI type | Source | Pipeline parameters | +| ------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| In read name | [Illumina BCL convert >3.7.5](https://emea.support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl_convert/bcl-convert-v3-7-5-software-guide-1000000163594-00.pdf) | `--with_umi --skip_umi_extract --umitools_umi_separator ":"` | +| In sequence | [Lexogen QuantSeq® 3’ mRNA-Seq V2 FWD](https://www.lexogen.com/quantseq-3mrna-sequencing) + [UMI Second Strand Synthesis Module](https://faqs.lexogen.com/faq/how-can-i-add-umis-to-my-quantseq-libraries) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P.{6})(?P.{4}).*"` | +| In sequence | [Lexogen CORALL® Total RNA-Seq V1](https://www.lexogen.com/corall-total-rna-seq/)
> _mind [Appendix H](https://www.lexogen.com/wp-content/uploads/2020/04/095UG190V0130_CORALL-Total-RNA-Seq_2020-03-31.pdf) regarding optional trimming_ | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P.{12}).*"`
Optional: `--clip_r2 9 --three_prime_clip_r2 12` | +| In sequence | Takara Bio [SMART-Seq Total RNA Pico Input with UMIs](https://www.takarabio.com/documents/User%20Manual/SMART/SMART-Seq%20Total%20RNA%20Pico%20Input%20with%20UMIs%20%28ZapR%20Mammalian%29%20User%20Manual.pdf) and [SMARTer® Stranded Total RNA-Seq Kit v3](https://www.takarabio.com/documents/User%20Manual/SMARTer%20Stranded%20Total%20RNA/SMARTer%20Stranded%20Total%20RNA-Seq%20Kit%20v3%20-%20Pico%20Input%20Mammalian%20User%20Manual-a_114950.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern2 "^(?P.{8})(?P.{6}).*"` | +| In sequence | [Watchmaker mRNA Library Prep Kit](https://watchmakergenomics.com/wp-content/uploads/2023/11/M223_mRNA-Library-Prep-Kit-_UG_WMUG214_v1-1-0823.pdf) with [Twist UMI Adapter System](https://www.twistbioscience.com/sites/default/files/resources/2023-03/DOC-001337_TechNote-ProcessingSequencingDataUtilizingUMI-REV1-singles.pdf) | `--with_umi --umitools_extract_method "regex" --umitools_bc_pattern "^(?P.{5})(?P.{2}).*" --umitools_bc_pattern2 "^(?P.{5})(?P.{2}).*"` | > _No warranty for the accuracy or completeness of the parameters is implied_