From b0f6c1a3a03d503eb4b07baa2a1cf1dfe31ec3f6 Mon Sep 17 00:00:00 2001 From: a-slide Date: Wed, 27 Oct 2021 23:26:42 +0100 Subject: [PATCH] main doc update --- NanoCount/__init__.py | 2 +- README.md | 4 ++-- docs/index.md | 6 +++--- meta.yaml | 2 +- setup.py | 2 +- versipy.yaml | 2 +- versipy_history.txt | 1 + 7 files changed, 10 insertions(+), 9 deletions(-) diff --git a/NanoCount/__init__.py b/NanoCount/__init__.py index 4a19332..fbaa5cd 100755 --- a/NanoCount/__init__.py +++ b/NanoCount/__init__.py @@ -1,7 +1,7 @@ # -*- coding: utf-8 -*- __name__ = "NanoCount" -__version__ = "1.0.0.post1" +__version__ = "1.0.0.post2" __description__ = "NanoCount estimates transcripts abundance from Oxford Nanopore *direct-RNA sequencing* datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads" __url__ = "https://github.com/a-slide/NanoCount/" __licence__ = "MIT" diff --git a/README.md b/README.md index 3286f40..94e4f61 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ -# NanoCount v1.0.0.post1 +# NanoCount v1.0.0.post2 ![NanoCount](./docs/pictures/NanoCount.png) @@ -15,7 +15,7 @@ **NanoCount estimates transcripts abundance from Oxford Nanopore *direct-RNA sequencing* datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads** -Full documentation is available at https://a-slide.github.io/NanoCount/ +Full documentation is available at https://adrienleger.com/NanoCount/ --- diff --git a/docs/index.md b/docs/index.md index 5a2301f..105c806 100644 --- a/docs/index.md +++ b/docs/index.md @@ -1,4 +1,4 @@ -# Welcome to NanoCount v1.0.0.post1 documentation +# Welcome to NanoCount v1.0.0.post2 documentation [NanoCount](pictures/NanoCount.png) @@ -22,8 +22,8 @@ #### Align reads -Reads should be aligned to a **transcriptome reference** using **[minimap2](https://github.com/lh3/minimap2)**. -We recommend using the `-N 10` option to retain at least 10 secondary mappings. +Reads must be aligned a transcriptome reference using minimap2 with `-p 0 -N 10` options to retain up to 10 secondary mappings without filtering. +NanoCount will take care of the low score alignments internally. ``` minimap2 -t 4 -ax map-ont -p 0 -N 10 transcriptome.fa.gz reads.fastq.gz | samtools view -bh > aligned_reads.bam diff --git a/meta.yaml b/meta.yaml index 4fbc9f3..6b0a313 100644 --- a/meta.yaml +++ b/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.0.0.post1" %} +{% set version = "1.0.0.post2" %} {% set name = "NanoCount" %} package: diff --git a/setup.py b/setup.py index c798e00..783bed3 100755 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ setup( name="NanoCount", description="NanoCount estimates transcripts abundance from Oxford Nanopore *direct-RNA sequencing* datasets, using an expectation-maximization approach like RSEM, Kallisto, salmon, etc to handle the uncertainty of multi-mapping reads", - version="1.0.0.post1", + version="1.0.0.post2", long_description=long_description, long_description_content_type="text/markdown", url="https://github.com/a-slide/NanoCount/", diff --git a/versipy.yaml b/versipy.yaml index 140468a..c3fc498 100644 --- a/versipy.yaml +++ b/versipy.yaml @@ -5,7 +5,7 @@ version: a: null b: null rc: null - post: 1 + post: 2 dev: null managed_values: __package_name__: NanoCount diff --git a/versipy_history.txt b/versipy_history.txt index d226160..20aa5d3 100644 --- a/versipy_history.txt +++ b/versipy_history.txt @@ -19,3 +19,4 @@ 2021-09-10 19:44:30.726193 0.4.0.post4 minor doc update 2021-10-26 10:14:30.076292 1.0.0 Release before paper publication in NAR 2021-10-27 09:39:27.221554 1.0.0.post1 minor doc change +2021-10-27 23:26:41.943187 1.0.0.post2 main doc update