Hopefully someone can help me with this one.
I am using Bowtie2 and BWA to do an alignment of paired fastq files from Illumina HiSeq2000.
When i open the SAM files produced, the big difference i notice is on the SAM field 11 corresponding to the read qualities.
here is how the stuff looks - i am pasting the first read and as you can see from the results, the mapping quality is different: 42 against 37 which i understand as the algorithms are different but when it comes to the SAM field 11 its so different ! Now i've read that Bowtie is aware of base quality and bwa is not, but can anyone explain to me what did BWA write in this 11th field of my sam file.
bowtie2: (settings: --end-to-end --very-fast )
SRR385642.1 73 chr14 21216082 42 101M = 21216082 0 ACANAGAGCAGAAGCTTCAGCTACATTGAATTCCATTGTGGCGTAGATGGATATGTTGATAACATAGAAGACCTGAGGATTATAGAACCTATCAGCAANAN 380#2>/+138678.@@56?=972486:7:.'22*/*8+=74<(6;0%770//'8((1**4163(/./10-,'**20%/5350(001//6.+..**11#(# AS:i:-5 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:3G94C0T0A0 YT:Z:UP RG:Z:@RGtID:SRR385642tLB:ExercisetSM:1tPL:ILLUMINA
bwasettings: standard, i run bwa aln on each fast, and then bwa sampe to get the SAM)
SRR385642.1 73 chr14 21216082 37 101M = 21216082 0 ACANAGAGCAGAAGCTTCAGCTACATTGAATTCCATTGTGGCGTAGATGGATATGTTGATAACATAGAAGACCTGAGGATTATAGAACCTATCAGCAANAN
^T^Y^Q^D^S^_^P^L^R^T^Y^W^X^Y^O!!^V^W ^^^Z^X^S^U^Y^WESC^XESC^O^H^S^S^K^P^K^Y^L^^^X^U^] ^W^\^Q^F^X^X^Q^P^P^H^Y ^R^K^K^U^R^W^T ^P^O^P^R^Q^N^M^H^K^K^S^Q^F^P^V^T^V^Q ^Q^Q^R^P^P^W^O^L^O^O^K^K
^R^R^D ^D RG:Z:SRR385642 XT:A:U NM:i:4 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:4 XO:i:0 XG:i:0 MD:Z:3G94C0T0A0
Thank you very much!
I am using Bowtie2 and BWA to do an alignment of paired fastq files from Illumina HiSeq2000.
When i open the SAM files produced, the big difference i notice is on the SAM field 11 corresponding to the read qualities.
here is how the stuff looks - i am pasting the first read and as you can see from the results, the mapping quality is different: 42 against 37 which i understand as the algorithms are different but when it comes to the SAM field 11 its so different ! Now i've read that Bowtie is aware of base quality and bwa is not, but can anyone explain to me what did BWA write in this 11th field of my sam file.
bowtie2: (settings: --end-to-end --very-fast )
SRR385642.1 73 chr14 21216082 42 101M = 21216082 0 ACANAGAGCAGAAGCTTCAGCTACATTGAATTCCATTGTGGCGTAGATGGATATGTTGATAACATAGAAGACCTGAGGATTATAGAACCTATCAGCAANAN 380#2>/+138678.@@56?=972486:7:.'22*/*8+=74<(6;0%770//'8((1**4163(/./10-,'**20%/5350(001//6.+..**11#(# AS:i:-5 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:3G94C0T0A0 YT:Z:UP RG:Z:@RGtID:SRR385642tLB:ExercisetSM:1tPL:ILLUMINA
bwasettings: standard, i run bwa aln on each fast, and then bwa sampe to get the SAM)
SRR385642.1 73 chr14 21216082 37 101M = 21216082 0 ACANAGAGCAGAAGCTTCAGCTACATTGAATTCCATTGTGGCGTAGATGGATATGTTGATAACATAGAAGACCTGAGGATTATAGAACCTATCAGCAANAN
^T^Y^Q^D^S^_^P^L^R^T^Y^W^X^Y^O!!^V^W ^^^Z^X^S^U^Y^WESC^XESC^O^H^S^S^K^P^K^Y^L^^^X^U^] ^W^\^Q^F^X^X^Q^P^P^H^Y ^R^K^K^U^R^W^T ^P^O^P^R^Q^N^M^H^K^K^S^Q^F^P^V^T^V^Q ^Q^Q^R^P^P^W^O^L^O^O^K^K
^R^R^D ^D RG:Z:SRR385642 XT:A:U NM:i:4 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:4 XO:i:0 XG:i:0 MD:Z:3G94C0T0A0
Thank you very much!
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