BWA和Bowtie2默认参数比对结果

一直认为bwa和bowtie2比对差异比较大，比对一组数据时均使用默认参数如下
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的比对结果

image.png

比对率为15.2%~52.4%，除去未比对上的reads，single mapped reads最多。
看下bwa的比对结果

image.png
每个样品的比对率均高于Bowtie2

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选几个未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

这条read使用bowtie2比对，只有paired-end一条read比对上，而bwa两条均能比对上，另一条比对为41T4T53，还有很多类似情况就不一一举例了
如果直接使用默认参数的话，两个的差距还是挺大的