Dear Heng, I recently aligned paired short reads to genome sequences using command "bwa aln -t 10 -I genome.fa LM-180_trim.1.fastq > LM-180_trim.1.sai; bwa aln -t 10 -I genome.fa LM-180_trim.2.fastq > LM-180_trim.2.sai ; bwa sampe -s genome.fa LM-180_trim.1.sai LM-180_trim.2.sai LM-180_trim.1.fastq LM-180_trim.2.fastq > LM-180_trim.sam". However, I could't convert the sam file to bam format file use command "samtools view -bS LM-180_trim.sam -o LM-180_trim.bam". The error information "[samopen] SAM header is present: 34218 sequences. Parse error at line 34221: sequence and quality are inconsistent" was reported. I checked the sam file and found that the quality score were change campared with raw data. I don't why. The accessory file recorded a example data from "LM-180_trim.sam" file. Thank you! Best wishesMing Lei
bwa_out.sam
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