I ran SOAPdenovo on some paired end Illumina gDNA reads. I am interested in
the contigs. I looked at the .contig file and I see the descriptions have
something called cvg and tip. For example,
Is cvg the coverage? Is it the average sequencing depth per base (i.e.,
normalized by contig length), or the number of reads aligning to the whole
contig?
Also, there are a whole bunch of short contigs with zero coverage. I am
assuming these don't show up in the scaffolds and should be thrown away
before any downstream analyses?
Hi
I ran SOAPdenovo on some paired end Illumina gDNA reads. I am interested in
the contigs. I looked at the .contig file and I see the descriptions have
something called cvg and tip. For example,
Is cvg the coverage? Is it the average sequencing depth per base (i.e.,
normalized by contig length), or the number of reads aligning to the whole
contig?
Also, there are a whole bunch of short contigs with zero coverage. I am
assuming these don't show up in the scaffolds and should be thrown away
before any downstream analyses?
Thank you for your time.