I've tried two different header styles in my input FASTQ headers when running BWA:
@SN7001163:162:C4A1UACXX:1:1101:1062:2076/1
and
@SN7001163:162:C4A1UACXX:1:1101:1062:2076 1:N:0:GTCCGCA
My goal is to be able to tell which mate I'm looking at in the FASTQ file, but it seems to get stripped in the SAM output, where from "bwa sampe" I get lines like this:
How can I tell which of these alignment lines refers to which input mate?
@SN7001163:162:C4A1UACXX:1:1101:1062:2076/1
and
@SN7001163:162:C4A1UACXX:1:1101:1062:2076 1:N:0:GTCCGCA
My goal is to be able to tell which mate I'm looking at in the FASTQ file, but it seems to get stripped in the SAM output, where from "bwa sampe" I get lines like this:
Code:
SN7001163:162:C4A1UACXX:1:1101:1062:2076 77 * 0 0 * * 0 0 GTTTGCTTGGCTGTGAGCTTGTCCGACACGGGCCACCAGGAGAGTGAGATACACCGAGACGAGCATCCTGTCTTTCTCTCGGACGGTTCCACAACAAATAA @?@DDD?;<;F>?<2A<E<FFC9:FE8):8@?FFF@FF=;=;D;).).7>77==EB'93;;3=@@:@(:3,+(4::@B>@5?-<@B<?<34>ABB1<8:43 SN7001163:162:C4A1UACXX:1:1101:1062:2076 141 * 0 0 * * 0 0 GCCATGTTGAGTGAGAATTTATTATTTGTTGTGGAACC ;<;;(42@9)@)84):46=69416)2@:@:<=1(66@?
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