I have a set of Illumina GA2 paired-end fastq files.
These reads of the fastqs has 76b length.
Before mapping, I trimmed barcode sequence from 5' end of both 1st and 2nd reads, finally, the reads have 63-67bp length.
BWA's author says following.
・reads < 70bp should be mapped by BWA-backtrack (BWA-backtrack can map 70bp< and <100bp reads, but they mention than these reads should be BWA-MEM algorithm.)
・reads > 100bp should be mapped by BWA-MEM. BWA-MEM algorithm is recommeded.
Any one has an idea which BWA-backtrack or BWA-MEM I should use?? Thanks!!!