Hi
I found a strange mapping result by Bioscope.
I analyzed the paried end reads from a whole transcriptome, and checked the mapping results.
Threre were a number of reads which were both properly mapped and unmapped at the same time.
For instance, a pair of reads (F3 & F5) '504_910_1119' were mapped poperly, however, there were extra alignments that the F3 was unmapped. I set the 'Alignment filter modes' as 'Primary', so the one best alignment was supposed to be selected among multi-hits. Is it a bug of Bioscope? Any one has observed this kind of results?
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504_910_1119 83 chr21 32600530 0 4H46M = 32600531 50 TTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA @IIIIB1=IIEIIIIHIIIIIIIIIIIIIIIIIIIIIII%%IIII; RG:Z:20110812083702784 NH:i:4 CM:i:3 SM:i:4 CQ:Z:;?;:?7%=;?;9:=929?5:<8==955=<790==:15===12==>3.;=< CS:Z:T3000030000000000000000000000000000000000000000000
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504_910_1119 163 chr21 32600531 0 25M10H = 32600530 -50 TTTTTTAAAAAAAAAAAAAAAAAAA IED86:IE//%%5,,%&-+*/=:/0 RG:Z:20110812083702784 NH:i:4 CM:i:2 SM:i:1 CQ:Z:B)=(1&5=)')%1%(%&''%&*4')(%7%%%%5(. CS:Z:G10000030000200003000000003303000020
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504_910_1119 69 * 0 0 * chr21 18218140 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN * RG:Z:20110812083702784 NH:i:4 CQ:Z:;?;:?7%=;?;9:=929?5:<8==955=<790==:15===12==>3.;=< CS:Z:T30000030000000000000000000000000000000000000000000
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504_910_1119 101 * 0 0 * chr21 34903877 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN * RG:Z:20110812083702784 NH:i:4 CQ:Z:;?;:?7%=;?;9:=929?5:<8==955=<790==:15===12==>3.;=<
CS:Z:T30000030000000000000000000000000000000000000000000
**********************************************************
I found a strange mapping result by Bioscope.
I analyzed the paried end reads from a whole transcriptome, and checked the mapping results.
Threre were a number of reads which were both properly mapped and unmapped at the same time.
For instance, a pair of reads (F3 & F5) '504_910_1119' were mapped poperly, however, there were extra alignments that the F3 was unmapped. I set the 'Alignment filter modes' as 'Primary', so the one best alignment was supposed to be selected among multi-hits. Is it a bug of Bioscope? Any one has observed this kind of results?
**********************************************************
504_910_1119 83 chr21 32600530 0 4H46M = 32600531 50 TTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA @IIIIB1=IIEIIIIHIIIIIIIIIIIIIIIIIIIIIII%%IIII; RG:Z:20110812083702784 NH:i:4 CM:i:3 SM:i:4 CQ:Z:;?;:?7%=;?;9:=929?5:<8==955=<790==:15===12==>3.;=< CS:Z:T3000030000000000000000000000000000000000000000000
**********************************************************
504_910_1119 163 chr21 32600531 0 25M10H = 32600530 -50 TTTTTTAAAAAAAAAAAAAAAAAAA IED86:IE//%%5,,%&-+*/=:/0 RG:Z:20110812083702784 NH:i:4 CM:i:2 SM:i:1 CQ:Z:B)=(1&5=)')%1%(%&''%&*4')(%7%%%%5(. CS:Z:G10000030000200003000000003303000020
**********************************************************
504_910_1119 69 * 0 0 * chr21 18218140 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN * RG:Z:20110812083702784 NH:i:4 CQ:Z:;?;:?7%=;?;9:=929?5:<8==955=<790==:15===12==>3.;=< CS:Z:T30000030000000000000000000000000000000000000000000
**********************************************************
504_910_1119 101 * 0 0 * chr21 34903877 0 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN * RG:Z:20110812083702784 NH:i:4 CQ:Z:;?;:?7%=;?;9:=929?5:<8==955=<790==:15===12==>3.;=<
CS:Z:T30000030000000000000000000000000000000000000000000
**********************************************************
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