HISAT2 new release --avoid-pseudogene

Hi all , i was wondering if any one has tried the updated hisat2 with --avoid-pseudogene below when I use it i do not see any significant difference in alignment.

Without --avoid-pseudogene summary

HISAT2 summary stats:
        Total pairs: 173658742
                Aligned concordantly or discordantly 0 time: 66605212 (38.35%)
                Aligned concordantly 1 time: 91369263 (52.61%)
                Aligned concordantly >1 times: 11872302 (6.84%)
                Aligned discordantly 1 time: 3811965 (2.20%)
        Total unpaired reads: 133210424
                Aligned 0 time: 99377802 (74.60%)
                Aligned 1 time: 27278723 (20.48%)
                Aligned >1 times: 6553899 (4.92%)
        Overall alignment rate: 71.39%

with --avoid-pseudogene

HISAT2 summary stats:
        Total pairs: 173658742
                Aligned concordantly or discordantly 0 time: 66605060 (38.35%)
                Aligned concordantly 1 time: 90353104 (52.03%)
                Aligned concordantly >1 times: 12888440 (7.42%)
                Aligned discordantly 1 time: 3812138 (2.20%)
        Total unpaired reads: 133210120
                Aligned 0 time: 99377861 (74.60%)
                Aligned 1 time: 27799698 (20.87%)
                Aligned >1 times: 6032561 (4.53%)
        Overall alignment rate: 71.39%

Does anyone see different trends?

rna-seq hisat2

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written 9.2 years ago by badribio

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