macでインフォマティクス

macでインフォマティクス

NGS関連のインフォマティクス情報についてまとめています。

pacbioのbamをfastqに変換する BAM2fastx

 

 

PacificBiosciences/bam2fastx Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files. by @PacificBiosciences - Repository | DevHub.io

 

BAM format specification for PacBio(5.1.0)

https://pacbiofileformats.readthedocs.io/en/5.1/BAM.html

 

インストール

依存

Github

#bioconda (link)
conda install -c bioconda bam2fastx

> bam2fasta -h

# bam2fasta -h

Usage: bam2fasta [options] INPUT

Converts multiple BAM and/or DataSet files into into gzipped FASTA file(s).

 

Options:

  -h,--help          Output this help.

  --version          Output version info.

  -o,--output        Prefix of output filenames

  -c                 Gzip compression level [1-9] [1]

  -u                 Do not compress. In this case, we will not add .gz, and we ignore any -c setting.

  --split-barcodes   Split output into multiple FASTA files, by barcode pairs.

  -p,--seqid-prefix  Prefix for sequence IDs in headers

 

Arguments:

  input              Input file.

 

> bam2fastq -h

# bam2fastq -h

Usage: bam2fastq [options] INPUT

Converts multiple BAM and/or DataSet files into into gzipped FASTQ file(s).

 

Options:

  -h,--help          Output this help.

  --version          Output version info.

  -o,--output        Prefix of output filenames

  -c                 Gzip compression level [1-9] [1]

  -u                 Do not compress. In this case, we will not add .gz, and we ignore any -c setting.

  --split-barcodes   Split output into multiple FASTQ files, by barcode pairs.

  -p,--seqid-prefix  Prefix for sequence IDs in headers

 

Arguments:

  input              Input file.

 

 

実行方法

subreads.bamを指定する。

bam2fasta -o projectName m54008_160330_053509.subreads.bam

 

引用

GitHub - PacificBiosciences/bam2fastx: Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files.

 

参考

Where is the documentation for PacBio tool bam2fastx?

https://www.biostars.org/p/387385/