Dear All,
I ran Flagstat under NGS: SAM Tools to check the quality of the Tophat
output (the file of accepted hits). I got the diagnosis results as follow:
9471730 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
9471730 + 0 mapped (100.00%:-nan%)
0 + 0 paired in sequencing
0
Hello Jianguang,
This is the expected output from this particular tool. Your TopHat
output file 'accepted hits' contains only mapped data.
I did notice this option for the TopHat run:
Is this library mate-paired?
Single-end
Your data was originally paired end - so this is unexpected. But
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