I am using both TASSEL4 and TASSEL5 with the same data set. I have noticed that the fastq file created by them(using FastqToTagCountPlugin and TagExportToFastqPlugin respectively) has a astounding difference in terms of number of reads.
I am curious to know what might be the difference in these two plugins? I am aware that TASSEL5 used a database format to store all the tags maybe it has to do something with the disparity? Also the number of variants called by TASSEL4 is naturally higher compared to TASSEL5
Anyone who has a clearcut idea regarding the same could perhaps shed some light on what makes TASSEL4 more lenient compared to TASSEL5?