removing sequencing gaps

Question

[cdwilliam524]

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!

[Devon Ryan]

I assume you mean that you mapped the short reads (fastq) to the reference genome (fasta), rather than the other way around.

Can you elaborate a bit on what you mean by gaps in the SAM file? I can think of a couple possible ways to interpret that.

[cdwilliam524]

Hi Devon,

I am new to bioinformatics, so it should be in the way you stated. Sorry for the confusion.

So in the *.sam file I have sequence like NNNNNNNNNCNNNNNNNTNNNNNNAGNNNNCT... I assume Ns are sequencing gaps and I want to remove them and I want to know the start/ end positions of the mapped contigs (I am not sure if I worded it right).

Thanks