hisat2-第一次使用-2019-07-08+解压

参考文章https://www.jianshu.com/p/250607bd401f；https://www.plob.org/article/11502.html；http://www.biotrainee.com/thread-2073-1-1.html

luoyang@DESKTOP-AO2ICCR:/mnt/d/AAA-台式机-LY-WorkSpace$ hisat2 -t -x grch38/genome -1 105TRA/105TRA_1.fq.gz -2 105TRA/105TRA_2.fq.gz -S aligned/105TRA.sam  # 命令行

以下是运行结果（用时1h+），最后得到.bam文件：

Time loading forward index: 00:00:17

Time loading reference: 00:00:02

Multiseed full-index search: 01:10:25

32339397 reads; of these:

  32339397 (100.00%) were paired; of these:

    1639696 (5.07%) aligned concordantly 0 times

    29704037 (91.85%) aligned concordantly exactly 1 time

    995664 (3.08%) aligned concordantly >1 times

    ----

    1639696 pairs aligned concordantly 0 times; of these:

      250243 (15.26%) aligned discordantly 1 time

    ----

    1389453 pairs aligned 0 times concordantly or discordantly; of these:

      2778906 mates make up the pairs; of these:

        1457983 (52.47%) aligned 0 times

        1219994 (43.90%) aligned exactly 1 time

        100929 (3.63%) aligned >1 times

97.75% overall alignment rate

Time searching: 01:10:28

Overall time: 01:10:45

注释：

其中的genome是index文件的前缀

105TRA.sam是生成sam文件的名字，保存在aligned文件夹中

下载完index后要解压（下载花了一晚上加一个上午）

luoyang@DESKTOP-AO2ICCR:/mnt/d/AAA-台式机-LY-WorkSpace$ tar -zvxf grch38.tar.gz  #  命令行

grch38/

grch38/genome.5.ht2

grch38/genome.2.ht2

grch38/make_grch38.sh

grch38/genome.3.ht2

grch38/genome.4.ht2

grch38/genome.7.ht2

grch38/genome.1.ht2

grch38/genome.6.ht2

grch38/genome.8.ht2

grch38开头的是解压后的文件，保存在grch38/文件夹中，关于Linux如何解压参考https://blog.csdn.net/capecape/article/details/78548723；