Skip to content

Minor update to Readme.md #47

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
wants to merge 2 commits into
base: master
Choose a base branch
from
Open

Minor update to Readme.md #47

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
7d0fa1a
fixed links in input
alanhoyle Oct 11, 2021
cbfef9f
fixed Releases tab link
alanhoyle Oct 11, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 14 additions & 10 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,15 +13,17 @@ Manuscript: https://doi.org/10.1093/bioinformatics/btz033
ABRA2 requires Java 8.

We recommend running from a pre-compiled release.
Go to the Releases tab to download a recent version.
Go to the [Releases tab](https://github.com/mozack/abra2/releases) to download a recent version.

### DNA

Sample command for DNA:

```java -Xmx16G -jar abra2.jar --in normal.bam,tumor.bam --out normal.abra.bam,tumor.abra.bam --ref hg38.fa --threads 8 --targets targets.bed --tmpdir /your/tmpdir > abra.log```
``` bash
java -Xmx16G -jar abra2.jar --in normal.bam,tumor.bam --out normal.abra.bam,tumor.abra.bam --ref hg38.fa --threads 8 --targets targets.bed --tmpdir /your/tmpdir > abra.log
```

The above accepts normal.bam and tumor.bam as input and outputs sorted realigned BAM files named normal.abra.bam and tumor.abra.bam
The above accepts `normal.bam` and `tumor.bam` as input and outputs sorted realigned BAM files named `normal.abra.bam` and `tumor.abra.bam`

* Input files must be sorted by coordinate and index
* Output files are sorted
Expand All @@ -30,19 +32,21 @@ The above accepts normal.bam and tumor.bam as input and outputs sorted realigned

### RNA

ABRA2 is capable of utilizing junction information to aid in assembly and realignment. It has been tested only on STAR output to date.
ABRA2 is capable of utilizing junction information to aid in assembly and realignment. It has been tested only on [STAR](https://github.com/alexdobin/STAR) output to date.

Sample command for RNA:

```java -Xmx16G -jar abra2.jar --in star.bam --out star.abra.bam --ref hg38.fa --junctions bam --threads 8 --gtf gencode.v26.annotation.gtf --dist 500000 --sua --tmpdir /your/tmpdir > abra2.log 2>&1```
``` bash
java -Xmx16G -jar abra2.jar --in star.bam --out star.abra.bam --ref hg38.fa --junctions bam --threads 8 --gtf gencode.v26.annotation.gtf --dist 500000 --sua --tmpdir /your/tmpdir > abra2.log 2>&1
```

Here, star.bam is the input bam file and star.abra.bam is the output bam file.
Here, `star.bam` is the input bam file and `star.abra.bam` is the output bam file.

Junctions observed during alignment can be passed in using the ```--junctions``` param. The input file format is similar to the SJ.out.tab file output by STAR. If ```bam``` is specified, ABRA2 will dynamically identify splice junctions from the BAM file on the fly. Note that the SJ.out.tab file contains only junctions deemed "high quality" by STAR. The complete set of all splice junctions can be identified using the program ```abra.cadabra.SpliceJunctionCounter```
Junctions observed during alignment can be passed in using the ```--junctions``` param. The input file format is similar to the `SJ.out.tab` file output by STAR. If ```bam``` is specified, ABRA2 will dynamically identify splice junctions from the BAM file on the fly. Note that the `SJ.out.tab` file contains only junctions deemed "high quality" by STAR. The complete set of all splice junctions can be identified using the program ```abra.cadabra.SpliceJunctionCounter```

Annotated junctions can be passed in using the ```--gtf``` param. See: https://www.gencodegenes.org/releases/current.html
It is beneficial to use both of the junction related options.
Annotated junctions can be passed in using the ```--gtf``` param. For human annotations, see: https://www.gencodegenes.org/human/releases.html

Known indels can be passed in using the --in-vcf argument. Unannotated junctions originally identified as splices by the aligner may be converted to deletions if a known deletion is matched. Consider this option if you have indels detected from DNA for the same sample / subject. It is not recommended to use large datasets when using this option (i.e. don't pass in dbSNP).
It is beneficial to use both of the junction related options.

Known indels can be passed in using the ```--in-vcf``` argument. Unannotated junctions originally identified as splices by the aligner may be converted to deletions if a known deletion is matched. Consider this option if you have indels detected from DNA for the same sample / subject. It is not recommended to use large datasets when using this option (i.e. don't pass in dbSNP).