比对软件测试
最后发布时间 : 2023-08-06 19:27:47
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学习资料
reads2是reads1的反向互补序列
reads_1.fq
@seq1 match
TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG
+
JIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJJIJJJJIJJIJJJJIJJI
使用下面命令生成reads2
echo "TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG" | rev | tr 'ATCG' 'TAGC'
reads_2.fq
@seq1 match
CAGCTCTCAAGCCCCTGGTCAGCAATCTGTCCACTAGCGCATCTTGTTCTTTGGCTTCA
+
JIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJJIJJIJJJJIJJIJJJJI
bowtie2
bowtie2 -x bowtie2/ref1.fa -1 reads_1.fq -2 reads_2.fq
1 reads; of these:
1 (100.00%) were paired; of these:
0 (0.00%) aligned concordantly 0 times
1 (100.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
0 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
0 pairs aligned 0 times concordantly or discordantly; of these:
0 mates make up the pairs; of these:
0 (0.00%) aligned 0 times
0 (0.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
100.00% overall alignment rate
@HD VN:1.5 SO:unsorted GO:query
@SQ SN:ref1 LN:105
@PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/home/wy/workspace/bowtie2-master/bowtie2-align-s --wrapper basic-0 -x bowtie2/ref1.fa -1 reads_1.fq -2 reads_2.fq"
seq1 99 ref1 15 42 59M = 15 59 TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG JIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJJIJJJJIJJIJJJJIJJI AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:59 YS:i:0 YT:Z:CP
seq1 147 ref1 15 42 59M = 15 -59 TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG IJJJJIJJIJJJJIJJIJJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJ AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:59 YS:i:0 YT:Z:CP
可以看到bowtie2的flag为
99- read paired (0x1)
- read mapped in proper pair (0x2)
- mate reverse strand (0x20)
- first in pair (0x40)
147- read paired (0x1)
- read mapped in proper pair (0x2)
- read reverse strand (0x10)
- second in pair (0x80)
bwa mem
bwa mem bwa/ref1.fa reads_1.fq reads_2.fq
[M::bwa_idx_load_from_disk] read 0 ALT contigs
@SQ SN:ref1 LN:105
@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa mem bwa/ref1.fa reads_1.fq reads_2.fq
[M::process] read 2 sequences (118 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 1, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 2 reads in 0.001 CPU sec, 0.001 real sec
seq1 97 ref1 15 60 59M = 15 59 TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG JIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJJIJJJJIJJIJJJJIJJI NM:i:0 MD:Z:59 MC:Z:59M AS:i:59 XS:i:0
seq1 145 ref1 15 60 59M = 15 -59 TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG IJJJJIJJIJJJJIJJIJJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJ NM:i:0 MD:Z:59 MC:Z:59M AS:i:59 XS:i:0
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem bwa/ref1.fa reads_1.fq reads_2.fq
[main] Real time: 0.002 sec; CPU: 0.005 sec
可以看到bwa mem 的flag为
97- read paired (0x1)
- mate reverse strand (0x20)
- first in pair (0x40)
145- read paired (0x1)
- read reverse strand (0x10)
- second in pair (0x80)
reads2与reads1完全相同
reads_1.fq
@seq1 match
TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG
+
JIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJJIJJJJIJJIJJJJIJJI
reads_2_discordantly.fq
@seq1 match
TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG
+
JIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJJIJJIJJJJIJJIJJJJI
bowtie2
bowtie2 -x bowtie2/ref1.fa -1 reads_1.fq -2 reads_2_discordantly.fq
1 reads; of these:
1 (100.00%) were paired; of these:
1 (100.00%) aligned concordantly 0 times
0 (0.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
1 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
1 pairs aligned 0 times concordantly or discordantly; of these:
2 mates make up the pairs; of these:
1 (50.00%) aligned 0 times
1 (50.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
50.00% overall alignment rate
@HD VN:1.5 SO:unsorted GO:query
@SQ SN:ref1 LN:105
@PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/home/wy/workspace/bowtie2-master/bowtie2-align-s --wrapper basic-0 -x bowtie2/ref1.fa -1 reads_1.fq -2 reads_2_discordantly.fq"
seq1 73 ref1 15 42 59M = 15 0 TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG JIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJJIJJJJIJJIJJJJIJJI AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:59 YT:Z:UP
seq1 133 ref1 15 0 * = 15 0 TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG JIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJJIJJIJJJJIJJIJJJJI YT:Z:UP
可以看到bowtie2的flag为
73- read paired (0x1)
- mate unmapped (0x8)
- first in pair (0x40)
133- read paired (0x1)
- read unmapped (0x4)
- second in pair (0x80)
bwa mem
bwa mem bwa/ref1.fa reads_1.fq reads_2_discordantly.fq
[M::bwa_idx_load_from_disk] read 0 ALT contigs
@SQ SN:ref1 LN:105
@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa mem bwa/ref1.fa reads_1.fq reads_2_discordantly.fq
[M::process] read 2 sequences (118 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 2 reads in 0.001 CPU sec, 0.001 real sec
seq1 65 ref1 15 60 59M = 15 0 TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG JIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJJIJJJJIJJIJJJJIJJI NM:i:0 MD:Z:59 MC:Z:59M AS:i:59 XS:i:0
seq1 129 ref1 15 60 59M = 15 0 TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG JIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJJIJJIJJJJIJJIJJJJI NM:i:0 MD:Z:59 MC:Z:59M AS:i:59 XS:i:0
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem bwa/ref1.fa reads_1.fq reads_2_discordantly.fq
[main] Real time: 0.002 sec; CPU: 0.005 sec
可以看到bwa mem 的flag为
65- read paired (0x1)
- first in pair (0x40)
129- read paired (0x1)
- second in pair (0x80)
reads2是reads1的互补序列
reads_1.fq
@seq1 match
TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG
+
JIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJJIJJJJIJJIJJJJIJJI
reads_2_discordantly.fq
@seq1 match
ACTTCGGTTTCTTGTTCTACGCGATCACCTGTCTAACGACTGGTCCCCGAACTCTCGAC
+
JIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJJIJJIJJJJIJJIJJJJI
bowtie2
bowtie2 -x bowtie2/ref1.fa -1 reads_1.fq -2 reads_2_tr.fq
1 reads; of these:
1 (100.00%) were paired; of these:
1 (100.00%) aligned concordantly 0 times
0 (0.00%) aligned concordantly exactly 1 time
0 (0.00%) aligned concordantly >1 times
----
1 pairs aligned concordantly 0 times; of these:
0 (0.00%) aligned discordantly 1 time
----
1 pairs aligned 0 times concordantly or discordantly; of these:
2 mates make up the pairs; of these:
1 (50.00%) aligned 0 times
1 (50.00%) aligned exactly 1 time
0 (0.00%) aligned >1 times
50.00% overall alignment rate
@HD VN:1.5 SO:unsorted GO:query
@SQ SN:ref1 LN:105
@PG ID:bowtie2 PN:bowtie2 VN:2.5.1 CL:"/home/wy/workspace/bowtie2-master/bowtie2-align-s --wrapper basic-0 -x bowtie2/ref1.fa -1 reads_1.fq -2 reads_2_tr.fq"
seq1 73 ref1 15 42 59M = 15 0 TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG JIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJJIJJJJIJJIJJJJIJJI AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:59 YT:Z:UP
seq1 133 ref1 15 0 * = 15 0 ACTTCGGTTTCTTGTTCTACGCGATCACCTGTCTAACGACTGGTCCCCGAACTCTCGAC JIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJJIJJIJJJJIJJIJJJJI YT:Z:UP
可以看到bowtie2的flag为
73- read paired (0x1)
- mate unmapped (0x8)
- first in pair (0x40)
133- read paired (0x1)
- read unmapped (0x4)
- second in pair (0x80)
bwa mem
bwa mem bwa/ref1.fa reads_1.fq reads_2_tr.fq
[M::bwa_idx_load_from_disk] read 0 ALT contigs
@SQ SN:ref1 LN:105
@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa mem bwa/ref1.fa reads_1.fq reads_2_tr.fq
[M::process] read 2 sequences (118 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 0, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] skip orientation FR as there are not enough pairs
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 2 reads in 0.001 CPU sec, 0.001 real sec
seq1 73 ref1 15 60 59M = 15 0 TGAAGCCAAAGAACAAGATGCGCTAGTGGACAGATTGCTGACCAGGGGCTTGAGAGCTG JIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJJIJJJJIJJIJJJJIJJI NM:i:0 MD:Z:59 AS:i:59 XS:i:0
seq1 133 ref1 15 0 * = 15 0 ACTTCGGTTTCTTGTTCTACGCGATCACCTGTCTAACGACTGGTCCCCGAACTCTCGAC JIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJIJJIJJJJJIJJIJJJJIJJIJJJJI MC:Z:59M AS:i:0 XS:i:0
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem bwa/ref1.fa reads_1.fq reads_2_tr.fq
[main] Real time: 0.002 sec; CPU: 0.005 sec
可以看到bwa mem 的flag为
73- read paired (0x1)
- mate unmapped (0x8)
- first in pair (0x40)
133- read paired (0x1)
- read unmapped (0x4)
- second in pair (0x80)
可以看到此时bwa mem的flag值与bowtie2相似