Question: What is acceptable optimal overall percentage of Hisat2?
gravatar for mathavanbioinfo
5 days ago by
mathavanbioinfo10 wrote:

Hello all please share you're valuable knowledge! I am doing RNA-seq for human sample, I got different overall alignment(Hisat2) rate my samples percentage are 90.12, 95.26, 90.71,94.72 Is they're any optimal value is they're to accepting or reject the overall percentage of hisat2, shall I continue farther stringTies with these results

rna-seq • 63 views
ADD COMMENTlink modified 5 days ago • written 5 days ago by mathavanbioinfo10

is the second one really 35.26 % aligned? that is very (worrying) low, all the ones with >90% are OK I think.

There is no optimal value, but as stated above >90% is OK, depends of course also a little from your sample setup (eg. a not so pure sample will of course have less)

ADD REPLYlink modified 5 days ago • written 5 days ago by lieven.sterck5.2k
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