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
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
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