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
#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
参考
Where is the documentation for PacBio tool bam2fastx?
