while converting the sam to bam file using samtools i get the following error: [samopen] SAM header is present: 279439 sequences. Parse error at line 31099973: sequence and quality are inconsistent
Below are the commands that i have used for alignment and sam to bam conversion:
bowtie2 -x reference_genome/indexed -1 sample_R1.fastq.gz -2 sample_R2_.fastq.gz -S aligned_PE.sam
samtools view -S -b aligned_PE.sam -o aligned_PE.bam
Could anyone give your suggestion to solve this..
Thanks in advance!!