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minor doc update
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a-slide committed Sep 10, 2021
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2 changes: 1 addition & 1 deletion NanoCount/__init__.py
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# -*- coding: utf-8 -*-

__name__ = "NanoCount"
__version__ = "0.4.0.post3"
__version__ = "0.4.0.post4"
__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"
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2 changes: 1 addition & 1 deletion README.md
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# NanoCount v0.4.0.post3
# NanoCount v0.4.0.post4

![NanoCount](./docs/pictures/NanoCount.png)

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7 changes: 4 additions & 3 deletions docs/index.md
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# Welcome to NanoCount v0.4.0.post3 documentation
# Welcome to NanoCount v0.4.0.post4 documentation

[NanoCount](pictures/NanoCount.png)

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#### Align reads

Reads must be aligned a transcriptome reference using minimap2 with `-N 10` options to retain up to 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 -N 10 transcriptome.fa.gz reads.fastq.gz | samtools view -bh > aligned_reads.bam
minimap2 -t 4 -ax map-ont -p 0 -N 10 transcriptome.fa.gz reads.fastq.gz | samtools view -bh > aligned_reads.bam
```

#### Estimate transcripts abundance with NanoCount
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2 changes: 1 addition & 1 deletion meta.yaml
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{% set version = "0.4.0.post3" %}
{% set version = "0.4.0.post4" %}
{% set name = "NanoCount" %}

package:
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2 changes: 1 addition & 1 deletion setup.py
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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="0.4.0.post3",
version="0.4.0.post4",
long_description=long_description,
long_description_content_type="text/markdown",
url="https://github.com/a-slide/NanoCount/",
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2 changes: 1 addition & 1 deletion versipy.yaml
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a: null
b: null
rc: null
post: 3
post: 4
dev: null
managed_values:
__package_name__: NanoCount
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1 change: 1 addition & 0 deletions versipy_history.txt
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2021-09-08 23:15:55.956351 0.4.0.post1 minor change to doc
2021-09-08 23:28:38.629321 0.4.0.post2 minor change to doc
2021-09-10 17:38:16.670671 0.4.0.post3 minor doc update
2021-09-10 19:44:30.726193 0.4.0.post4 minor doc update

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