一直認(rèn)為bwa和bowtie2比對(duì)差異比較大，比對(duì)一組數(shù)據(jù)時(shí)均使用默認(rèn)參數(shù)如下
BWA
bwa mem -t 4 Ensembl/03.BWA_index/chicken ../../01.QC/${i}/Clean*_1.fq.gz ../../01.QC/${i}/Clean*_2.fq.gz -o align.sam
Bowtie2
nohup bowtie2 -x Ensembl/02.Bowtie2_index/chicken -k 1 -1 ../../01.QC/${i}/Clean*_1.fq.gz -2 ../../01.QC/${i}/Clean*_1.fq.gz -S align.sam &
看下bowtie2的比對(duì)結(jié)果
image.png
比對(duì)率為15.2%~52.4%函荣，除去未比對(duì)上的reads从藤，single mapped reads最多。
看下bwa的比對(duì)結(jié)果
image.png
每個(gè)樣品的比對(duì)率均高于Bowtie2
選幾個(gè)未mapped的reads查看
# V300032513L2C001R0020005307
bowtie2
V300032513L2C001R0020005307 73 1 173752628 255 100M = 173752628 0 GACCAGAGAAGCTGGACTATGCCTAGTAGCTGAGGTAATATTTGAGAGGTTCCACAAGCTCAGTGAGATTATTTGGAAGTCACAGATGTTTAGACACTGG eeeeeeeec^eeeeeeeefefeeeeeefeeefWeedeee`feeededeedefebeeefeefdeeeceee\ffeeeaeefeeeeaeeZfeefefeeffefe AS:i:-6 XN:i:0XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:3G96 YT:Z:UP
V300032513L2C001R0020005307 133 1 173752628 0 * = 173752628 0 GACCAGAGAAGCTGGACTATGCCTAGTAGCTGAGGTAATATTTGAGAGGTTCCACAAGCTCAGTGAGATTATTTGGAAGTCACAGATGTTTAGACACTGG eeeeeeeec^eeeeeeeefefeeeeeefeeefWeedeee`feeededeedefebeeefeefdeeeceee\ffeeeaeefeeeeaeeZfeefefeeffefe YT:Z:UP
bwa
V300032513L2C001R0020005307 99 1 173752628 60 100M = 173752842 314 GACCAGAGAAGCTGGACTATGCCTAGTAGCTGAGGTAATATTTGAGAGGTTCCACAAGCTCAGTGAGATTATTTGGAAGTCACAGATGTTTAGACACTGG eeeeeeeec^eeeeeeeefefeeeeeefeeefWeedeee`feeededeedefebeeefeefdeeeceee\ffeeeaeefeeeeaeeZfeefefeeffefe NM:i:1 MD:Z:3G96 MC:Z:100M AS:i:96 XS:i:0
V300032513L2C001R0020005307 147 1 173752842 60 100M = 173752628 -314 AATGGCTTCACCTAAAATGCGGTGTAGGAAAGCCTTCAGAACCAAGCTGAAATGAACAAGAAAATAAGTTTCAGAAGTTTGCATTATTCATTTAAACTTA eefeffedfefffeeeeeeeffeefeeeeeeeeeeedefeeeeefefeeefeefeefefe]eefeeeee[efeefffeee]eeeeeeeeeeeeeeefefe NM:i:2 MD:Z:41T4T53 MC:Z:100M AS:i:90 XS:i:22
這條read使用bowtie2比對(duì)隅忿，只有paired-end一條read比對(duì)上养葵，而bwa兩條均能比對(duì)上征堪，另一條比對(duì)為41T4T53，還有很多類似情況就不一一舉例了
如果直接使用默認(rèn)參數(shù)的話关拒，兩個(gè)的差距還是挺大的
