From a146f9b2a0c459330a3470c3fe5548b4b51d600b Mon Sep 17 00:00:00 2001 From: Mark Izraelson Date: Thu, 9 May 2024 12:44:28 -0600 Subject: [PATCH] update --- docs/mixcr/getting-started/docker.md | 21 ++ docs/mixcr/reference/mixcr-assemble.md | 9 +- docs/mixcr/reference/mixcr-exportShmTrees.md | 3 - docs/mixcr/reference/mixcr-findAlleles.md | 56 ++-- docs/mixcr/reference/mixcr-groupClones.md | 37 +- docs/mixcr/reference/mixcr-mergeLibrary.md | 4 +- .../reference/overview-built-in-presets.md | 2 + .../idt-human-rna-bcr-umi-archer-dark.svg | 237 +++++++++++++ .../idt-human-rna-bcr-umi-archer-light.svg | 241 ++++++++++++++ .../idt-human-rna-tcr-umi-archer-dark.svg | 237 +++++++++++++ .../idt-human-rna-tcr-umi-archer-light.svg | 241 ++++++++++++++ docs/mixcr/reference/pics/pacbio-dark.svg | 314 +++++++++++++++++ docs/mixcr/reference/pics/pacbio-light.svg | 315 ++++++++++++++++++ .../takara-mouse-rna-bcr-umi-smarseq-dark.svg | 297 +++++++++++++++++ ...takara-mouse-rna-bcr-umi-smarseq-light.svg | 299 +++++++++++++++++ .../takara-sc-human-rna-tcr-smarter-dark.svg | 277 +++++++++++++++ .../takara-sc-human-rna-tcr-smarter-light.svg | 279 ++++++++++++++++ docs/mixcr/reference/presets/_idt.md_ | 52 +++ docs/mixcr/reference/presets/_pacbio.md_ | 32 ++ docs/mixcr/reference/presets/_takara.md_ | 61 ++++ 20 files changed, 2982 insertions(+), 32 deletions(-) create mode 100644 docs/mixcr/reference/pics/idt-human-rna-bcr-umi-archer-dark.svg create mode 100644 docs/mixcr/reference/pics/idt-human-rna-bcr-umi-archer-light.svg create mode 100644 docs/mixcr/reference/pics/idt-human-rna-tcr-umi-archer-dark.svg create mode 100644 docs/mixcr/reference/pics/idt-human-rna-tcr-umi-archer-light.svg create mode 100644 docs/mixcr/reference/pics/pacbio-dark.svg create mode 100644 docs/mixcr/reference/pics/pacbio-light.svg create mode 100644 docs/mixcr/reference/pics/takara-mouse-rna-bcr-umi-smarseq-dark.svg create mode 100644 docs/mixcr/reference/pics/takara-mouse-rna-bcr-umi-smarseq-light.svg create mode 100644 docs/mixcr/reference/pics/takara-sc-human-rna-tcr-smarter-dark.svg create mode 100644 docs/mixcr/reference/pics/takara-sc-human-rna-tcr-smarter-light.svg create mode 100644 docs/mixcr/reference/presets/_idt.md_ create mode 100644 docs/mixcr/reference/presets/_pacbio.md_ diff --git a/docs/mixcr/getting-started/docker.md b/docs/mixcr/getting-started/docker.md index 6a003899..b7a1c2b4 100644 --- a/docs/mixcr/getting-started/docker.md +++ b/docs/mixcr/getting-started/docker.md @@ -69,6 +69,27 @@ For those who rely on other tools inside the image, beware, new build relies on `mixcr` startup script is added to `PATH` environment variable, so even if you specify custom entrypoint, there is no need in using of full path to run `mixcr`. +## Using external libraries with docker + +To use an external library, place the `.json(.gz)` file in the same directory that you mount to `/work` inside Docker. Then use the `--library` parameter with the MiXCR command. In the example below, `/path/to/put/results` contains the `phocoena-IGH.json.gz` library file. + +```shell +docker run --rm \ + -e MI_LICENSE="...license-token..." \ + -v /path/to/raw/data:/raw:ro \ + -v /path/to/put/results:/work \ +ghcr.io/milaboratory/mixcr/mixcr:latest \ +mixcr analyze generic-amplicon \ + --library phocoena-IGH \ + --species phocoena \ + --rna \ + --rigid-left-alignment-boundary \ + --floating-right-alignment-boundary C \ + /raw/input_R1.fastq.gz \ + /raw/input_R2.fastq.gz \ + output +``` + ## License notice for IMGT images Images with IMGT reference library contain data imported from IMGT and is subject to terms of use listed on http://www.imgt.org site. diff --git a/docs/mixcr/reference/mixcr-assemble.md b/docs/mixcr/reference/mixcr-assemble.md index 7af689c0..da9abcf8 100644 --- a/docs/mixcr/reference/mixcr-assemble.md +++ b/docs/mixcr/reference/mixcr-assemble.md @@ -340,8 +340,11 @@ Parameters that control clustering procedure and determines the rules for the fr `-OcloneClusteringParameters.searchParameters=twoMismatchesOrIndels` : Parameters that control fuzzy match criteria between clones in adjacent layers. Available predefined values: `oneMismatch`, `oneIndel`, `oneMismatchOrIndel`, `twoMismatches`, `twoIndels`, `twoMismatchesOrIndels`, ..., `fourMismatchesOrIndels`. By default, `twoMismatchesOrIndels` allows two mismatches or indels (not more than two errors of both types) between two adjacent clones (parent and direct child). -`-OcloneClusteringParameters.clusteringFilter.specificMutationProbability=1E-3` -: Probability of a single nucleotide mutation in clonal sequence which has non-hypermutation origin (i.e. PCR or sequencing error). This parameter controls relative counts between two clones in adjacent layers: a smaller clone can be attached to a larger one if its count smaller than count of parent multiplied by `(clonalSequenceLength * specificMutationProbability) ^ numberOfMutations` +`-OcloneClusteringParameters.clusteringFilter.backgroundSubstitutionRate=0.002` and `-OcloneClusteringParameters.clusteringFilter.backgroundIndelRate=0.0002` +: These parameters set the error probability in case Phred quality is high. For example, if a `backgroundSubstitutionRate` is set to `0.001` and a Phred quality of a certain nucleotide is 20, which indicates the error probability of `0.01`, MiXCR will use `0.01`. If the Phred quality is 40 (error probability is `0.0001`, which is lower than the `backgroundSubstitutionRate`), MiXCR will use the `backgroundSubstitutionRate` and set the error probability to `0.002`. The higher the `backgroundSubstitutionRate` the more aggressive the correction will be. + +`-OcloneClusteringParameters.clusteringFilter.correctionPower=0.001` +: Indicates the False Discovery Rate for the correction process, approximating the percentage of actual sequences that might be compromised during correction. The default value is 0.001. Usage example: change maximum allowed number of mutations: ```shell @@ -355,4 +358,4 @@ Turn clustering off: ## Hardware recommendations -Assembly step is memory consuming. Reading and decompression of `.vdjca` file is handled in parallel and highly efficient way. MiXCR needs amount of RAM sufficient to store clonotype table in memory. In an exterme case of one million of full-length UMI-assembled clonotypes, it is recommended to supply at least 32GB of RAM. Speed almost does not scale with the increase of CPU. +Assembly step is memory consuming. Reading and decompression of `.vdjca` file is handled in parallel and highly efficient way. MiXCR needs amount of RAM sufficient to store clonotype table in memory. In an extreme case of one million of full-length UMI-assembled clonotypes, it is recommended to supply at least 32GB of RAM. Speed almost does not scale with the increase of CPU. diff --git a/docs/mixcr/reference/mixcr-exportShmTrees.md b/docs/mixcr/reference/mixcr-exportShmTrees.md index 530f3cb8..0f51a0b2 100644 --- a/docs/mixcr/reference/mixcr-exportShmTrees.md +++ b/docs/mixcr/reference/mixcr-exportShmTrees.md @@ -646,9 +646,6 @@ for the full list and formatting) `-isotype [(primary|subclass|auto)]` : Export isotype for IGH chains if it's distinguishable. `primary` will resolve 'IgA', 'IgD', 'IgG', 'IgE', 'IgM'. `subtype` will try resolve isotypes like 'IgA1' or 'IgA2'. Default `auto` will automatically decide whether to resolve the primary or subtype isotype based on the level of detail distinguishable for each clone. -`-topChains` -: Top chains - `-geneLabel