linux学习100篇37：转录组分析用软件及安装samtools

安装

(rnaseq) root 11:51:32 ~
$ conda install -y samtools
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.9.2
  latest version: 4.10.1

Please update conda by running

    $ conda update -n base -c defaults conda



## Package Plan ##

  environment location: /root/miniconda3/envs/rnaseq

  added / updated specs:
    - samtools


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    bzip2-1.0.8                |       h7f98852_4         484 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    libgcc-7.2.0               |       h69d50b8_2         304 KB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
    samtools-1.7               |                1         1.0 MB  https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/bioconda
    ------------------------------------------------------------
                                           Total:         1.8 MB

The following NEW packages will be INSTALLED:

  bzip2              anaconda/cloud/conda-forge/linux-64::bzip2-1.0.8-h7f98852_4
  libgcc             anaconda/cloud/conda-forge/linux-64::libgcc-7.2.0-h69d50b8_2
  samtools           anaconda/cloud/bioconda/linux-64::samtools-1.7-1



Downloading and Extracting Packages
libgcc-7.2.0         | 304 KB    | ######################################## | 100% 
bzip2-1.0.8          | 484 KB    | ######################################## | 100% 
samtools-1.7         | 1.0 MB    | ######################################## | 100% 
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(rnaseq) root 11:53:05 ~

查看

(rnaseq) root 11:53:05 ~
$ samtools

Program: samtools (Tools for alignments in the SAM format)
Version: 1.7 (using htslib 1.7)

Usage:   samtools  [options]

Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     index          index alignment

  -- Editing
     calmd          recalculate MD/NM tags and '=' bases
     fixmate        fix mate information
     reheader       replace BAM header
     targetcut      cut fosmid regions (for fosmid pool only)
     addreplacerg   adds or replaces RG tags
     markdup        mark duplicates

  -- File operations
     collate        shuffle and group alignments by name
     cat            concatenate BAMs
     merge          merge sorted alignments
     mpileup        multi-way pileup
     sort           sort alignment file
     split          splits a file by read group
     quickcheck     quickly check if SAM/BAM/CRAM file appears intact
     fastq          converts a BAM to a FASTQ
     fasta          converts a BAM to a FASTA

  -- Statistics
     bedcov         read depth per BED region
     depth          compute the depth
     flagstat       simple stats
     idxstats       BAM index stats
     phase          phase heterozygotes
     stats          generate stats (former bamcheck)

  -- Viewing
     flags          explain BAM flags
     tview          text alignment viewer
     view           SAM<->BAM<->CRAM conversion
     depad          convert padded BAM to unpadded BAM

(rnaseq) root 11:54:46 ~
(rnaseq) root 11:55:13 ~
$ samtools --help

Program: samtools (Tools for alignments in the SAM format)
Version: 1.7 (using htslib 1.7)

Usage:   samtools  [options]

Commands:
  -- Indexing
     dict           create a sequence dictionary file
     faidx          index/extract FASTA
     index          index alignment

  -- Editing
     calmd          recalculate MD/NM tags and '=' bases
     fixmate        fix mate information
     reheader       replace BAM header
     targetcut      cut fosmid regions (for fosmid pool only)
     addreplacerg   adds or replaces RG tags
     markdup        mark duplicates

  -- File operations
     collate        shuffle and group alignments by name
     cat            concatenate BAMs
     merge          merge sorted alignments
     mpileup        multi-way pileup
     sort           sort alignment file
     split          splits a file by read group
     quickcheck     quickly check if SAM/BAM/CRAM file appears intact
     fastq          converts a BAM to a FASTQ
     fasta          converts a BAM to a FASTA

  -- Statistics
     bedcov         read depth per BED region
     depth          compute the depth
     flagstat       simple stats
     idxstats       BAM index stats
     phase          phase heterozygotes
     stats          generate stats (former bamcheck)

  -- Viewing
     flags          explain BAM flags
     tview          text alignment viewer
     view           SAM<->BAM<->CRAM conversion
     depad          convert padded BAM to unpadded BAM

(rnaseq) root 11:55:29 ~