Thread: [Bio-bwa-help] Missing quality scores
Status: Beta
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From: <cl...@ma...> - 2010-06-10 19:28:07
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Hi, I have encountered a problem while using bwa aligner. After using bwa on fastq files I checked the sam file for the reads with missing quality e.g. "*", and got quite many () . Fastq files have quality information on those reads. Here is one of examples of the read in fastq and in sam format: Fastq: @SOLEXA-DELL_0060:6:44:18581:16891#0/1 CAAGCAGTCAGTGGGATGGGGAGCATCTTCCGCAAGAAATGGGGGTGTTTAAGGAGGCCCCCAAGATGAGCTAAAA +SOLEXA-DELL_0060:6:44:18581:16891#0/1 ffffffffffffffffffffefffffffffffffffffffcfeff^`^ddaddddddfddededdddc_^\bb^cd Sam: SOLEXA-DELL_0060:6:44:18581:16891#0 99 chr1 159308947 60 76M = 159309107 236 CAAGCAGTCAGTGGGATGGGGAGCATCTTCCGCAAGAAATGGGGGTGTTTAAGGAGGCCCCCAAGATGAGCTAAAA * XT:A:U NM:i:0 SM:i:37 AM:i:37 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:76 RG:Z:OP2.2L06 My question is why the value for the quality is missing in sam file? Sincerely, Egor. |