Hi, all
Recently I have a paired-end data from Illumina/Solexa sequencing machine. My sequencing DNA fragments are about 100-300 bp, and my read length is 125 bp for one end of the pairs. My question is, if the dovetail pairs are general in my data? Do I need to consider these pairs as concordant pairs in the Bowtie2 alignment?
I have tried to specify "--dovetail" parameter in Bowtie2, and it has 10% more concordant pairs in the alignment compared to the results without "--dovetail".
Without "--dovetail":
With "--dovetail":
Hope to receive your suggestions, thanks.
wisense
Recently I have a paired-end data from Illumina/Solexa sequencing machine. My sequencing DNA fragments are about 100-300 bp, and my read length is 125 bp for one end of the pairs. My question is, if the dovetail pairs are general in my data? Do I need to consider these pairs as concordant pairs in the Bowtie2 alignment?
I have tried to specify "--dovetail" parameter in Bowtie2, and it has 10% more concordant pairs in the alignment compared to the results without "--dovetail".
Without "--dovetail":
Code:
30047395 reads; of these: 30047395 (100.00%) were paired; of these: 7364630 (24.51%) aligned concordantly 0 times 18847070 (62.72%) aligned concordantly exactly 1 time 3835695 (12.77%) aligned concordantly >1 times 75.49% overall alignment rate
Code:
30047395 reads; of these: 30047395 (100.00%) were paired; of these: 4190935 (13.95%) aligned concordantly 0 times 21610905 (71.92%) aligned concordantly exactly 1 time 4245555 (14.13%) aligned concordantly >1 times 86.05% overall alignment rate
wisense
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