I am doing a RNA-Seq analysis and want to map my reads back to the assembly I got from Trinity. Below are my commands. I was hoping to get a single output file named low1.bam. Instead I got a lot of tmp files named like below: samtools.40306.3656.tmp.0000.bam, samtools.40306.3656.tmp.0001.bam ...
bowtie2 --local --no-unal -x Trinity.fasta -q -1 low1_S3_L001_R1_001.fastq -2 low1_S3_L001_R2_001.fastq -p 20 \ | samtools view -Sb - \ | samtools sort -o - - > low1.bam
I am using the latest bowtie2 and samtools version.