Hello,
I have paired-end Illumina reads, now the depth of sequencing is 100x and I've found the plasmid consisted of one full-length contig. I'd like to check if depth 50x is good enough for my aims. How could I do it?
A lot of thanks, Valery
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v.shapovalova1 •
khmer can do digital normalization to 50x, though 100x is not too crazy in terms of sequencing depth.
Thank you very much! seems that it's what I'm looking for. am i right that it'll removereads with the same indexes from formard file and reverse file?
That is correct. Everything is explained in the protocol.
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Remove half of the reads and repeat the process. That is called subsampling.
I suppose that i need the same reads for forwars and reverse for assembly. So i need to take indexes. No?
what are your aims? just the assembly?
Yes. I'd like to check the assembly with lower amount of reads. But i suppose that the indexes from forward and reverse should be the same. like in this post: Selecting Random Pairs From Fastq?