我對編碼很陌生，所以我不確定如何解決這個問題。我想查看我們獲得的一些資料并使用 Bismark 對它們進行排序。我已經使用 Trim Galore 來減少讀取，現在我想將資料匯入 Bismark。但是，我不確定如何處理這個問題。在檔案中它說它需要運行 Perl，所以我從 github 下載了 Perl 和 Bismark zip 檔案。我還下載了 bowtie2 zip 檔案并將兩個 zip 檔案解壓縮到同一目錄中。然后我打開 Perl 命令提示符并將目錄設定為包含我提取的檔案夾的目錄。我把這一行放在：
> \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.
將目錄更改為 Bismark 檔案夾后，我也嘗試了此操作：
> 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
我嘗試了其他一些事情，但總而言之，我對如何解決這個問題感到有些困惑。我現在下載的東西：
俾斯麥 zip 檔案 - https://github.com/FelixKrueger/Bismark
Bowtie2 zip 檔案 - https://github.com/BenLangmead/bowtie2
.fa 格式的基因組組裝
我想以fasta格式分析的資料
任何見解都會有所幫助。
uj5u.com熱心網友回復：
我認為Bismark并且bowtie2只原生支持 Linux 和 macOS。如果您想bismark在 Windows上使用，您可以嘗試通過 *nix 仿真系統（如Cygwin、 ）安裝它MSYS2，或者干脆使用 WSL。我在帶有 WSL 和 Ubuntu 20.04 的 Windows 11 上對此進行了測驗：
下載bowtie2-2.4.4-linux-x86_64.zip并解壓到
~/bowtie2/bowtie2-2.4.4-linux-x86_64檔案夾。下載Bismark-0.23.1.zip并解壓到
~/bismark/Bismark-0.23.1/測驗安裝：
$ 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>} [...]
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