Could anyone tell me how to remove sequencing gaps from a *.sam file?
I use bwa to map the reference genome (fasta) to the metatranscriptome files (fastq), and then use "bwa sampe" to combine all the *.fasta, *.sai, and *.fastq to get the *.sam file. But the *sam file contains many gaps between contigs. How could I remove them?
Thanks in advance!