https://github.com/nanoporetech/spliced_bam2gff
https://github.com/nanoporetech/spliced_bam2gff
Last synced: over 1 year ago
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- Host: GitHub
- URL: https://github.com/nanoporetech/spliced_bam2gff
- Owner: nanoporetech
- License: other
- Created: 2020-11-26T19:46:20.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2021-08-04T10:21:19.000Z (almost 5 years ago)
- Last Synced: 2025-04-06T08:02:15.834Z (over 1 year ago)
- Language: Go
- Size: 16 MB
- Stars: 5
- Watchers: 16
- Forks: 2
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE.md
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README
-----------------------------
spliced_bam2gff - a tool to convert spliced BAM alignments into GFF2 format
===========================================================================
[](https://anaconda.org/bioconda/spliced_bam2gff)
The **spliced_bam2gff** tool converts [BAM](https://samtools.github.io/hts-specs/SAMv1.pdf) alignments, produced by spliced aligners (such as [minimap2](https://github.com/lh3/minimap2), [gmap](http://research-pub.gene.com/gmap)), into a [GFF2](https://www.ensembl.org/info/website/upload/gff.html) format.
By default, introns are created based on the `N` cigar feature. Alternatively, if `-d` (i.e. for deletion) is specified, any deletions larger than the limit will be classified as an intron.
The orientation of the GFF2 features is determined by the `XS` strand tag and SAM flags depending on the aligner.
The tool supports splitting the output into *loci* and *bundles of loci* with a minimum number of features, which enables easy parallelisation of downstream analyses.
The generated GFF2 files can be compared to a reference annotation using the [gffcompare](https://github.com/gpertea/gffcompare) tool.
## Installation
The best way to install the tool is from bioconda:
- Make sure you have [miniconda3](https://docs.conda.io/en/latest/miniconda.html) installed.
- Set up the bioconda channel according to the [instructions](://bioconda.github.io/user/install.html).
- Install the tool by issuing `conda install spliced_bam2gff`
## Usage
```
Usage of ./spliced_bam2gff:
-L string
Write output partitioned into "loci" to this directory. Turns of output to stdout.
-M Input is from minimap2.
-S Do NOT discard secondary and supplementary alignments.
-V Print out version.
-b int
Bundle together loci in batches with at least this size. (default -1)
-d int
Classify all deletions larger than this as introns (-1 means off). (default -1)
-g Use strand tag as feature orientation then read strand if not available.
-h Print out help message.
-s Use read strand (from BAM flag) as feature orientation.
-t int
Number of cores to use. (default 8)
```
Examples
========
### Convert alignments generated by `minmap2 -x splice`
```
spliced_bam2gff -M ./test_data/sirv_simulated.bam > ./test_data/sirv_simulated_mm2.gff
```
Convert while classifying all deletions larger than 20 as introns:
```
spliced_bam2gff -d 20 -M ./test_data/sirv_simulated.bam > ./test_data/sirv_simulated_mm2.gff
```
Convert to GFF2 and split the output into loci separated by regions with no coverage:
```
spliced_bam2gff -M -L ./test_data/sirv_simulated_mm2_loci -s ./test_data/sirv_simulated.bam
```
Convert to GFF2 and split the output into bundles of loci with at least two thousand features:
```
spliced_bam2gff -b 2000 -M -L ./test_data/sirv_simulated_mm2_loci -s ./test_data/sirv_simulated.bam
```
### Convert alignments generated by `gmap`
```
spliced_bam2gff -g ./test_data/sirv_errors_gmap.bam > ./test_data/test_out_err.gff
```
Running tests
============
For running tests the following dependencies have to be installed:
- [gffcompare](https://github.com/gpertea/gffcompare)
Which is easy to install using [bioconda](https://bioconda.github.io).
Look into the `Makefiles` for targets testing the tools on simulated and real data.
Help
====
## Licence and Copyright
(c) 2020 Oxford Nanopore Technologies Ltd.
This Source Code Form is subject to the terms of the Mozilla Public
License, v. 2.0. If a copy of the MPL was not distributed with this
file, You can obtain one at http://mozilla.org/MPL/2.0/.
## FAQs and tips
- The [GFF2](https://www.ensembl.org/info/website/upload/gff.html) files can be visualised using [IGV](http://software.broadinstitute.org/software/igv).
- The GFF2 files can be converted to GFF3 or GTF using the [gffread](https://bioconda.github.io/recipes/gffread/README.html) utility.
## References and Supporting Information
See the post announcing the tool at the Oxford Nanopore Technologies community [here](https://community.nanoporetech.com/posts/new-transcriptomics-analys).