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lines changed Original file line number Diff line number Diff line change @@ -91,9 +91,9 @@ The `--umitools_grouping_method` parameter affects [how similar, but non-identic
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#### Examples:
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- | UMI type | Source | Pipeline parameters |
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- | ------------ | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------- |
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- | 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 ":" ` |
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+ | UMI type | Source | Pipeline parameters |
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+ | ------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------- |
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+ | 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 ":" ` |
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| 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<umi_1>.{6})(?P<discard_1>.{4}).*" ` |
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| In sequence | [ Lexogen CORALL® Total RNA-Seq V1] ( https://www.lexogen.com/corall-total-rna-seq/ ) <br > > _ 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<umi_1>.{12}).*" ` <br >Optional: ` --clip_r2 9 --three_prime_clip_r2 12 ` |
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| 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<umi_1>.{8})(?P<discard_1>.{6}).*" ` |
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