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Merge pull request DaehwanKimLab#336 from DaehwanKimLab/3ndoc
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Edit hisat-3n webpage for new feature: Zf tag and hisat-3n-table stdout
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imzhangyun authored Nov 8, 2021
2 parents c54f3d4 + 6b9d4f5 commit 67c5942
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17 changes: 8 additions & 9 deletions docs/_pages/hisat-3n.md
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Expand Up @@ -141,11 +141,10 @@ HISAT-3N uses the HISAT2 argument but has some extra arguments. Please check [HI
hisat-3n -x genome -q -U read.fq -S alignment_result.sam --base-change C,T --repeat



#### Extra SAM tags generated by HISAT-3N:

* `Yf:i:<N>`: Number of conversions are detected in the read.

* `Zf:i:<N>`: Number of un-converted bases are detected in the read. `Yf` + `Zf` = total number of bases which can be converted in the read sequence.
* `YZ:A:<A>`: The value `+` or `` indicate the read is mapped to REF-3N (`+`) or REF-RC-3N (`-`).

Generate a 3N-conversion-table with `hisat-3n-table`
Expand All @@ -162,17 +161,17 @@ Use `samtools sort` to convert the SAM file to a sorted SAM file.
Generate 3N-conversion-table with `hisat-3n-table`:

### Usage
hisat-3n-table [options]* --alignments <alignmentFile> --ref <refFile> --output-name <outputFile> --base-change <char1,char2>
hisat-3n-table [options]* --alignments <alignmentFile> --ref <refFile> --base-change <char1,char2>

#### Main arguments
* `--alignments <alignmentFile>`
SORTED SAM file. Please enter `-` for standard input.

* `--ref <refFile>`
The reference genome file (FASTA format) for generating HISAT-3N index.

* `--output-name <outputFile>`
Filename to write 3N-conversion-table (tsv format) to.
Filename to write 3N-conversion-table (tsv format) to. By default, table is written to the “standard out” or “stdout” filehandle (i.e. the console).

* `--base-change <char1,char2>`
The base-change rule. User should enter the exact same `--base-change` arguments in hisat-3n.
Expand All @@ -188,9 +187,6 @@ Generate 3N-conversion-table with `hisat-3n-table`:
* `-c/--CG-only`
Only count the CpG sites in reference genome. This option is designed for bisulfite sequencing reads.

* `-p/--threads <int>`
Launch `int` parallel threads (default: 1) for table building.

* `--added-chrname`
Please add this option if you use `--add-chrname` during `hisat-3n` alignment.
During `hisat-3n` alignment, the prefix "chr" is added in front of chromosome name and shows on SAM output, when user choose `--add-chrname`.
Expand All @@ -203,10 +199,13 @@ Generate 3N-conversion-table with `hisat-3n-table`:
`hisat-3n-table` cannot find the chromosome name on reference because it has no "chr" prefix. This option is to help `hisat-3n-table`
find the matching chromosome name on reference file. The 3n-table provides the same chromosome name as SAM file.

#### Other options:
* `-p/--threads <int>`
Launch `int` parallel threads (default: 1) for table building.

* `-h/--help`
Print usage information and quit.


#### Examples:
# Generate the 3N-conversion-table for bisulfite sequencing data:
hisat-3n-table -p 16 --alignments sorted_alignment_result.sam --ref genome.fa --output-name output.tsv --base-change C,T
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