How does aligner determine strandness when doing alignment
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4.0 years ago
CY ▴ 740

This is maybe a silly question. But I just realize that the FASTQ contains both DNA reads of both strand (forward and reverse). However when doing alignment, the strandness of each read is not provided. How does aligner determine the strandness of reads? I am sensing I missed something here.

alignment • 735 views
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bwa help page says this:

Since version 0.6, BWA has been able to work with a reference genome longer than 4GB. This feature makes it possible to integrate the forward and reverse complemented genome in one FM-index, which speeds up both BWA-short and BWA-SW. As a tradeoff, BWA uses more memory because it has to keep all positions and ranks in 64-bit integers, twice larger than 32-bit integers used in the previous versions.

bwa paper says " The reverse complemented read sequence is processed at the same time". So bwa was probably RC'ing the reads when originally released but now may not be doing that. Someone will need to look in the code and confirm.

bowtie/bowtie2 store forward and reverse copies in separate index files.

BBMap concatenates the reference chromosomes in a long string. Since it stores its index in a special file format I am not sure if it is storing RC index copy or not.

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