Question: removing sequencing gaps
0
gravatar for cdwilliam524
5.4 years ago by
cdwilliam52430
United States
cdwilliam52430 wrote:

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! 

sequencing alignment • 1.5k views
ADD COMMENTlink written 5.4 years ago by cdwilliam52430

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.

ADD REPLYlink written 5.4 years ago by Devon Ryan93k

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

ADD REPLYlink written 5.4 years ago by cdwilliam52430
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