fastp质控完，接着用hisat2对比
先在hisat2官网
下载相应物种index
for i in {52..61};do hisat2 -p 24 -x ~/1data/hisat2index/rn6/genome -1 ~/1data/03fastp/SRR31837${i}_1.fastq.gz -2 ~/1data/03fastp/SRR31837${i}_2.fastq.gz -S ~/1data/04sam/${i}.sam;done
这一步最吃CPU，多线程服务器U能较快出结果
系统监视器_013.png
96.19% overall alignment rate
32774635 reads; of these:
32774635 (100.00%) were paired; of these:
2021610 (6.17%) aligned concordantly 0 times
24330986 (74.24%) aligned concordantly exactly 1 time
6422039 (19.59%) aligned concordantly >1 times
----
2021610 pairs aligned concordantly 0 times; of these:
62532 (3.09%) aligned discordantly 1 time
----
1959078 pairs aligned 0 times concordantly or discordantly; of these:
3918156 mates make up the pairs; of these:
2563226 (65.42%) aligned 0 times
1067508 (27.25%) aligned exactly 1 time
287422 (7.34%) aligned >1 times
96.09% overall alignment rate
45428825 reads; of these:
45428825 (100.00%) were paired; of these:
4558717 (10.03%) aligned concordantly 0 times
33674424 (74.13%) aligned concordantly exactly 1 time
7195684 (15.84%) aligned concordantly >1 times
----
4558717 pairs aligned concordantly 0 times; of these:
146448 (3.21%) aligned discordantly 1 time
----
4412269 pairs aligned 0 times concordantly or discordantly; of these:
8824538 mates make up the pairs; of these:
5645765 (63.98%) aligned 0 times
2559058 (29.00%) aligned exactly 1 time
619715 (7.02%) aligned >1 times
93.79% overall alignment rate
40521991 reads; of these:
40521991 (100.00%) were paired; of these:
4266423 (10.53%) aligned concordantly 0 times
30143618 (74.39%) aligned concordantly exactly 1 time
6111950 (15.08%) aligned concordantly >1 times
----
4266423 pairs aligned concordantly 0 times; of these:
139303 (3.27%) aligned discordantly 1 time
----
4127120 pairs aligned 0 times concordantly or discordantly; of these:
8254240 mates make up the pairs; of these:
5257939 (63.70%) aligned 0 times
2454656 (29.74%) aligned exactly 1 time
541645 (6.56%) aligned >1 times
93.51% overall alignment rate
36824255 reads; of these:
36824255 (100.00%) were paired; of these:
2130388 (5.79%) aligned concordantly 0 times
27299306 (74.13%) aligned concordantly exactly 1 time
7394561 (20.08%) aligned concordantly >1 times
----
2130388 pairs aligned concordantly 0 times; of these:
69769 (3.27%) aligned discordantly 1 time
----
2060619 pairs aligned 0 times concordantly or discordantly; of these:
4121238 mates make up the pairs; of these:
2662211 (64.60%) aligned 0 times
1148684 (27.87%) aligned exactly 1 time
310343 (7.53%) aligned >1 times
96.39% overall alignment rate
36152664 reads; of these:
36152664 (100.00%) were paired; of these:
2174607 (6.02%) aligned concordantly 0 times
26482101 (73.25%) aligned concordantly exactly 1 time
7495956 (20.73%) aligned concordantly >1 times
----
2174607 pairs aligned concordantly 0 times; of these:
67704 (3.11%) aligned discordantly 1 time
----
2106903 pairs aligned 0 times concordantly or discordantly; of these:
4213806 mates make up the pairs; of these:
2692086 (63.89%) aligned 0 times
1164355 (27.63%) aligned exactly 1 time
357365 (8.48%) aligned >1 times
96.28% overall alignment rate
60233649 reads; of these:
60233649 (100.00%) were paired; of these:
3476469 (5.77%) aligned concordantly 0 times
46526105 (77.24%) aligned concordantly exactly 1 time
10231075 (16.99%) aligned concordantly >1 times
----
3476469 pairs aligned concordantly 0 times; of these:
142229 (4.09%) aligned discordantly 1 time
----
3334240 pairs aligned 0 times concordantly or discordantly; of these:
6668480 mates make up the pairs; of these:
4370031 (65.53%) aligned 0 times
1844853 (27.67%) aligned exactly 1 time
453596 (6.80%) aligned >1 times
96.37% overall alignment rate
50632275 reads; of these:
50632275 (100.00%) were paired; of these:
2975330 (5.88%) aligned concordantly 0 times
39885109 (78.77%) aligned concordantly exactly 1 time
7771836 (15.35%) aligned concordantly >1 times
----
2975330 pairs aligned concordantly 0 times; of these:
87244 (2.93%) aligned discordantly 1 time
----
2888086 pairs aligned 0 times concordantly or discordantly; of these:
5776172 mates make up the pairs; of these:
3787949 (65.58%) aligned 0 times
1589637 (27.52%) aligned exactly 1 time
398586 (6.90%) aligned >1 times
96.26% overall alignment rate
56448363 reads; of these:
56448363 (100.00%) were paired; of these:
3323368 (5.89%) aligned concordantly 0 times
42721563 (75.68%) aligned concordantly exactly 1 time
10403432 (18.43%) aligned concordantly >1 times
----
3323368 pairs aligned concordantly 0 times; of these:
131951 (3.97%) aligned discordantly 1 time
----
3191417 pairs aligned 0 times concordantly or discordantly; of these:
6382834 mates make up the pairs; of these:
4193576 (65.70%) aligned 0 times
1728219 (27.08%) aligned exactly 1 time
461039 (7.22%) aligned >1 times
96.29% overall alignment rate
47639124 reads; of these:
47639124 (100.00%) were paired; of these:
2983577 (6.26%) aligned concordantly 0 times
35822480 (75.20%) aligned concordantly exactly 1 time
8833067 (18.54%) aligned concordantly >1 times
----
2983577 pairs aligned concordantly 0 times; of these:
124675 (4.18%) aligned discordantly 1 time
----
2858902 pairs aligned 0 times concordantly or discordantly; of these:
5717804 mates make up the pairs; of these:
3677457 (64.32%) aligned 0 times
1633875 (28.58%) aligned exactly 1 time
406472 (7.11%) aligned >1 times
96.14% overall alignment rate
经过服务器一晚努力工作得到10个sam文件，共447.4Gb
04sam_014.png
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