Skip to content
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

Fixing small typo in general-user-options.md #7

Open
wants to merge 1 commit into
base: master
Choose a base branch
from
Open

Fixing small typo in general-user-options.md #7

Changes from all commits
Commits
Show all changes
1 commit
Select commit
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
6 changes: 3 additions & 3 deletions doc/general-user-options.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,14 +13,14 @@ Other filtering can also be set up according to users’ requirements:

| Option | Description | Default |
|--------------------------------|-------------|-------------------------|
| `--gtffile` or `-b` | Specifies the path to the genome [annotation](https://github.com/vrmelo/SPLICE-q/wiki/Annotation-Files) file provided by GENCODE or Ensembl in GTF. | - |
| `--bamfile` or `-g` | Specifies the path to sequencing alignment file in BAM format. | - |
| `--gtffile` or `-g` | Specifies the path to the genome [annotation](https://github.com/vrmelo/SPLICE-q/wiki/Annotation-Files) file provided by GENCODE or Ensembl in GTF. | - |
| `--bamfile` or `-b` | Specifies the path to sequencing alignment file in BAM format. | - |
| `--outfile` or `-o` | Specifies an output file name and location. | ./splicing-efficiency.tsv |
| `--ChromsList` or `-x` | List of Chromosome names separated by comma (without spaces). | chr1-720, I-XVI, 2L, 2R, 3L, 3R, Z, W. |
| `--MinCoverage` or `-c` | Minimum number of reads spanning each splice junction. | 10 |
| `--MinReadQuality` or `-r` | Mapping quality. By default, only uniquely mapped reads are included. | >10 |
| `--MinIntronLength` or `-l` | Minimum intron length. Default value is optimal for analysis using human RNA-seq data. | 30 |
| `--FilterLevel` or `-f` | [Levels of restrictiveness](https://github.com/vrmelo/SPLICE-q/wiki/Overlap-of-genomic-elements) for strand-specific filtering: <br />1 - Keep all introns in the genome regardless of overlaps with other genomic elements. <br /> 2 - Select only introns whose splice junctions do not overlap any exon in different genes. <br /> 3 - Select only introns that do not overlap with any exon of the same or different gene. | 3 |
| `--IERatio` or `-i` | Running mode that additionally outputs the Inverse Intron Expression Ratio (IER). Restricted by _--FilterLevel 3_. | - |
| `--NProcesses` or `-p` | Multiple concurrent processes are used to minimize running times and the number of processes can be adjusted by the user through this parameter. Generates an index (BAI) file if not available. | 4 |
| `--NrProcesses` or `-p` | Multiple concurrent processes are used to minimize running times and the number of processes can be adjusted by the user through this parameter. Generates an index (BAI) file if not available. | 4 |
| `--quiet` or `-q` | Reduces verbosity. | - |