Hello, there,
I recently examined the output of tophat (tophat22.0.8) after converting them into sam file, and found that the following results:
grep "HWI-ST514:143982632:C37PRACXX:5:1101:12852:4786" accepted_hits.ns.sam
HWI-ST514:143982632:C37PRACXX:5:1101:12852:4786 89 A_ref-1.0_Cont33 766585 50 92M * 0 0 CTTGTATTGAGTACGATCTCTCCACCTCTCCGGTTCGCAATACAGCTTTGAGAAAGAACTTATTACCCTCTCTACTATATAATTAAATTGTA DDDDEDDDDDDDDDDDBDCDDDAACDDFHHJJJJJJJJIIHHJJJJJJJJJJJJJJJIJJIHFC:JJHGIIJJIJJJJJJJJJJJJJHHHFF MD:Z:92 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 YT:Z:UU
HWI-ST514:143982632:C37PRACXX:5:1101:12852:4786 137 A_ref-1.0_Cont33 766582 50 100M * 0 0 TTCCTTGTATTGAGTACGATCTCTCCACCTCTCCGGTTCGCAATACAGCTTTGAGAAAGAACTTATTACCCTCTCTACTATATAATTAAATTGTACTTTG CCCFFFFFHHHHHJGIIJJJJJJJJJJJJIJIIJJJFGIIJJJJJJJJIJHIJJJJJJJJHHHHHFFFFFFFDEEEEDEDEDEFEEEECCEDCCDEEFED MD:Z:100 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 YT:Z:UU
The reference is the genome scaffolds here. My question is about the samflag: 89 represents read paired,mate unmapped,read reverse strand,first in pair; 137 represents read paired, mate unmapped, second in pair.
These reads appear to be paired, and both mapped. Then why did samflag say their mates were not mapped? Is it because they did not map to the same scaffold?
Could anyone explain this to me?
Thanks
I recently examined the output of tophat (tophat22.0.8) after converting them into sam file, and found that the following results:
grep "HWI-ST514:143982632:C37PRACXX:5:1101:12852:4786" accepted_hits.ns.sam
HWI-ST514:143982632:C37PRACXX:5:1101:12852:4786 89 A_ref-1.0_Cont33 766585 50 92M * 0 0 CTTGTATTGAGTACGATCTCTCCACCTCTCCGGTTCGCAATACAGCTTTGAGAAAGAACTTATTACCCTCTCTACTATATAATTAAATTGTA DDDDEDDDDDDDDDDDBDCDDDAACDDFHHJJJJJJJJIIHHJJJJJJJJJJJJJJJIJJIHFC:JJHGIIJJIJJJJJJJJJJJJJHHHFF MD:Z:92 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 YT:Z:UU
HWI-ST514:143982632:C37PRACXX:5:1101:12852:4786 137 A_ref-1.0_Cont33 766582 50 100M * 0 0 TTCCTTGTATTGAGTACGATCTCTCCACCTCTCCGGTTCGCAATACAGCTTTGAGAAAGAACTTATTACCCTCTCTACTATATAATTAAATTGTACTTTG CCCFFFFFHHHHHJGIIJJJJJJJJJJJJIJIIJJJFGIIJJJJJJJJIJHIJJJJJJJJHHHHHFFFFFFFDEEEEDEDEDEFEEEECCEDCCDEEFED MD:Z:100 XG:i:0 NH:i:1 NM:i:0 XM:i:0 XN:i:0 XO:i:0 AS:i:0 YT:Z:UU
The reference is the genome scaffolds here. My question is about the samflag: 89 represents read paired,mate unmapped,read reverse strand,first in pair; 137 represents read paired, mate unmapped, second in pair.
These reads appear to be paired, and both mapped. Then why did samflag say their mates were not mapped? Is it because they did not map to the same scaffold?
Could anyone explain this to me?
Thanks
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