我如何 运行 这个 Bismark 亚硫酸氢盐测序程序？
How do I run this Bismark Bisulfite Sequencing program?
我对编码还很陌生，所以我不太确定如何处理这个问题。我想查看我们获得的一些数据并使用 Bismark 对它们进行排序。我已经使用 Trim Galore 来减少读取，现在我想将数据导入 Bismark。但是，我不确定如何处理这个问题。在文档中它说 运行 需要 Perl，所以我从 github 下载了 Perl 和 Bismark zip 文件。我还下载了 bowtie2 zip 文件并将这两个 zip 文件解压缩到同一目录中。然后我打开 Perl 命令提示符并将目录设置为包含我提取的文件夹的目录。
我把这一行放在：
> \bismark\bismark_genome_preparation --path_to_bowtie ^
C:\Users\sevro\Documents\Lab_Code\bowtie2-master --verbose ^
C:\Users\sevro\Documents\Lab_Code\genome
The system cannot find the path specified.
我在将目录更改为 Bismark 文件夹后也尝试了这个：
> perl bismark
Failed to execute Bowtie 2 porperly (return code of 'bowtie2 --version' was 256).
Please install Bowtie 2 or HISAT2 first and make sure it is in the PATH,
or specify the path to the Bowtie 2 with --path_to_bowtie2 /path/to/bowtie2,
or --path_to_hisat2 /path/to/hisat2
我尝试了一些其他的东西，但总的来说，我对如何解决这个问题有点困惑。我现在下载的东西：
俾斯麦 zip 文件- https://github.com/FelixKrueger/Bismark
Bowtie2 zip 文件- https://github.com/BenLangmead/bowtie2
.fa 格式的基因组组装
我要分析的fasta格式的数据
任何见解都会有所帮助。
我认为 Bismark 和 bowtie2 只支持 Linux 和 macOS。如果你想在 Windows 上使用 bismark，你可以尝试通过像 Cygwin、MSYS2 这样的 *nix 仿真系统安装它，或者简单地使用 WSL。我在 Windows 11 上用 WSL 和 Ubuntu 20.04:
测试了这个
已下载 bowtie2-2.4.4-linux-x86_64.zip 并提取到 ~/bowtie2/bowtie2-2.4.4-linux-x86_64 文件夹。
已下载 Bismark-0.23.1.zip 并提取到 ~/bismark/Bismark-0.23.1/
测试安装：
$ perl --version
This is perl 5, version 30, subversion 0 (v5.30.0) built for x86_64-linux-gnu-thread-multi (with 50 registered patches, see perl -V for more detail)
$ perl bismark --path_to_bowtie2 ../../bowtie2/bowtie2-2.4.4-linux-x86_64/Bowtie 2 seems to be working fine (tested command '../../bowtie2/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4])
Output format is BAM (default)
Did not find Samtools on the system. Alignments will be compressed with GZIP instead (.sam.gz)
Genome folder was not specified!
DESCRIPTION
The following is a brief description of command line options and arguments to control the Bismark
bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the
reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand
version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand).
Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome
(C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the
forward strand, by doing this alignments will produce the same positions). These 4 instances of Bowtie 2 or HISAT2
are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original
sequence from the genome and determine if there were any protected C's present or not.
The final output of Bismark is in BAM/SAM format by default, described in more detail below.
USAGE: bismark [options] <genome_folder> {-1 <mates1> -2 <mates2> | <singles>}
[...]
我对编码还很陌生，所以我不太确定如何处理这个问题。我想查看我们获得的一些数据并使用 Bismark 对它们进行排序。我已经使用 Trim Galore 来减少读取，现在我想将数据导入 Bismark。但是，我不确定如何处理这个问题。在文档中它说 运行 需要 Perl，所以我从 github 下载了 Perl 和 Bismark zip 文件。我还下载了 bowtie2 zip 文件并将这两个 zip 文件解压缩到同一目录中。然后我打开 Perl 命令提示符并将目录设置为包含我提取的文件夹的目录。 我把这一行放在：
> \bismark\bismark_genome_preparation --path_to_bowtie ^
C:\Users\sevro\Documents\Lab_Code\bowtie2-master --verbose ^
C:\Users\sevro\Documents\Lab_Code\genome
The system cannot find the path specified.
我在将目录更改为 Bismark 文件夹后也尝试了这个：
> perl bismark
Failed to execute Bowtie 2 porperly (return code of 'bowtie2 --version' was 256).
Please install Bowtie 2 or HISAT2 first and make sure it is in the PATH,
or specify the path to the Bowtie 2 with --path_to_bowtie2 /path/to/bowtie2,
or --path_to_hisat2 /path/to/hisat2
我尝试了一些其他的东西，但总的来说，我对如何解决这个问题有点困惑。我现在下载的东西：
俾斯麦 zip 文件- https://github.com/FelixKrueger/Bismark
Bowtie2 zip 文件- https://github.com/BenLangmead/bowtie2
.fa 格式的基因组组装
我要分析的fasta格式的数据
任何见解都会有所帮助。
我认为 Bismark 和 bowtie2 只支持 Linux 和 macOS。如果你想在 Windows 上使用 bismark，你可以尝试通过像 Cygwin、MSYS2 这样的 *nix 仿真系统安装它，或者简单地使用 WSL。我在 Windows 11 上用 WSL 和 Ubuntu 20.04:
已下载 bowtie2-2.4.4-linux-x86_64.zip 并提取到
~/bowtie2/bowtie2-2.4.4-linux-x86_64文件夹。已下载 Bismark-0.23.1.zip 并提取到
~/bismark/Bismark-0.23.1/测试安装：
$ perl --version This is perl 5, version 30, subversion 0 (v5.30.0) built for x86_64-linux-gnu-thread-multi (with 50 registered patches, see perl -V for more detail) $ perl bismark --path_to_bowtie2 ../../bowtie2/bowtie2-2.4.4-linux-x86_64/Bowtie 2 seems to be working fine (tested command '../../bowtie2/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Did not find Samtools on the system. Alignments will be compressed with GZIP instead (.sam.gz) Genome folder was not specified! DESCRIPTION The following is a brief description of command line options and arguments to control the Bismark bisulfite mapper and methylation caller. Bismark takes in FastA or FastQ files and aligns the reads to a specified bisulfite genome. Sequence reads are transformed into a bisulfite converted forward strand version (C->T conversion) or into a bisulfite treated reverse strand (G->A conversion of the forward strand). Each of these reads are then aligned to bisulfite treated forward strand index of a reference genome (C->T converted) and a bisulfite treated reverse strand index of the genome (G->A conversion of the forward strand, by doing this alignments will produce the same positions). These 4 instances of Bowtie 2 or HISAT2 are run in parallel. The sequence file(s) are then read in again sequence by sequence to pull out the original sequence from the genome and determine if there were any protected C's present or not. The final output of Bismark is in BAM/SAM format by default, described in more detail below. USAGE: bismark [options] <genome_folder> {-1 <mates1> -2 <mates2> | <singles>} [...]