I'm trying to extract sequences from a reference based assembly (the reference is a transcriptome) based on coverage and length in CLC. So, I want to extract the sequences with >5x coverage and >200bp. This is simple enough for de novo assembly (extract subset), is there something like this for ref-based?
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When you run "map reads to reference" you should selected the option "Create stand-alone read mappings" (in the last wizard step)
The output will be table that is very similar as the the novo output and you can extract a subset. -
Hi
I have a similar problem but with contigs ,I want to extract sequences between the contigs when the contigs are aligned to a refrence..how do I extract these sequences..Comment
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NGS has revolutionized clinical microbiology by offering new ways to identify and surveil pathogens without prior knowledge of the target. One popular approach is 16S rRNA and ITS amplicon sequencing, which targets specific microbial markers. But studies are increasingly incorporating shotgun metagenomics, a technique that sequences all DNA from a sample without targeting specific microbial markers. This approach allows more detailed taxonomic classification,...10-30-2026, 06:46 AM
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