Software to analyze Diamond data

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6.5 years ago

cupplesa • 0

I have generated a diamond file by aligning a set of genes to a set of shotgun sequencing data.

Could you recommend a software to analyze the data? The file is too big to manipulate in excel.

I have tried Megan, but this seems to use only KEGG, SEED etc, not a set of predefined genes.

alignment • 1.4k views

ADD COMMENT • link 6.5 years ago by cupplesa • 0

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You need to add additional clarification as to what exactly you are doing.

Are you referring to DIAMOND that is used as a BLAST+ replacement to do blastx searches? Why were you aligning known genes to shotgun sequences (rather than other way around)? What kind of known genes are these (NCBI nr)?

ADD REPLY • link 6.5 years ago by GenoMax 141k

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Hey, guys. I am having the same issue. I have aligned a set of shotgun sequencing data against nearly 600 genes using DIAMOND blastx. I want to know which genes are present and which are absent in my shotgun sequencing data! Do you have any recommendation how can I do it?

ADD REPLY • link 6.3 years ago by Ana ▴ 200

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