[galaxy-user] Please help me check the quality of the Tophat mapping to reference genome

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

Re: [galaxy-user] Please help me check the quality of the Tophat mapping to reference genome

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