Hello, there,
I used tophat to map the reads to the genome reference and the got the aligned bam file. I have a question about the following reads:
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grep "HWI-ST514:143982632:C37PRACXX:7:1101:10044:92913" accepted_hits.bam.sam
HWI-ST514:143982632:C37PRACXX:7:1101:10044:92913 97 A_Cont6 926942 50 61M102N4M A_Cont42 348362 0 TCACATGCTCGACCCTGCTCATGCTTCGCTCATCGAAAAGGCTCAGTTCTTCTACATCGCTGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:65 NM:i:0 XS:A:+ NH:i:1
HWI-ST514:143982632:C37PRACXX:7:1101:10044:92913 153 A_Cont6 926970 50 33M102N32M * 0 0 CTCATCGAAAAGGCTCAGTTCTTCTACATCGCTGGATTCTTCTTGACTGTCTCGCCTCCATCAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:65 NM:i:0 XS:A:+ NH:i:1
====
My understanding is that these two reads are paired. For the first read, according to the flag value and field 7 (A_Cont42), its mate should be mapped, indicating the both reads are mapped. However, for the second read, flag value and field 7(*) indicate that its mate is not mapped.
I feel there is discrepancy here. Could anyone help me figure out why?
Thanks a lot!
I used tophat to map the reads to the genome reference and the got the aligned bam file. I have a question about the following reads:
====
grep "HWI-ST514:143982632:C37PRACXX:7:1101:10044:92913" accepted_hits.bam.sam
HWI-ST514:143982632:C37PRACXX:7:1101:10044:92913 97 A_Cont6 926942 50 61M102N4M A_Cont42 348362 0 TCACATGCTCGACCCTGCTCATGCTTCGCTCATCGAAAAGGCTCAGTTCTTCTACATCGCTGGAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:65 NM:i:0 XS:A:+ NH:i:1
HWI-ST514:143982632:C37PRACXX:7:1101:10044:92913 153 A_Cont6 926970 50 33M102N32M * 0 0 CTCATCGAAAAGGCTCAGTTCTTCTACATCGCTGGATTCTTCTTGACTGTCTCGCCTCCATCAAT IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII AS:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:65 NM:i:0 XS:A:+ NH:i:1
====
My understanding is that these two reads are paired. For the first read, according to the flag value and field 7 (A_Cont42), its mate should be mapped, indicating the both reads are mapped. However, for the second read, flag value and field 7(*) indicate that its mate is not mapped.
I feel there is discrepancy here. Could anyone help me figure out why?
Thanks a lot!
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