Hello, I have clean and trimmed fastq files with an average of 150nt per read. I have tried BWA aln and also BWA mem for the alignment with my reference genome.
The alignment take around 2 days to process but ends u with 92kb file each time. I have changed algorithm from aln to mem, tried default parameters, tried clean fq and trimmed fq seperately. but same result all the time. Here are the commands that i used:
bwa index -a is ref.fna bwa aln ref.fna 1.fastq >1.aln bwa aln ref.fna 2.fastq >2.aln both files yileded alignment but when i used sampe: bwa sampe -P ref.fna 1.aln 2.aln 1.fastq 2.fastq > sample.sam.all it yielded 92kb
Later i tried BWA mem bwa mem -t 24 -M ref.fna trimmed-files1/1P.fastq trimmed-files1/2P.fastq >sample.sam 2> mem-pe.log also yielded 92kb file.
I cannot understand the reason. I checked the quality and it is all good.
Your help is appreciated. Qurat