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knights-lab / BugBase

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paired-end shotgun reads OTU picking with the IMG reference sequences #4

Closed chenminicode closed 6 years ago

chenminicode commented 6 years ago

Hi, I'm trying to use paired-end shotgun reads, picking OTU with the IMG reference sequences. The command shogun_bugbase -i path_to_sequences -o output_path -u path_to_shogun_bugbase_db, -i option support fna file input, I have paired-end fastq reads, should I merge read1 and read2 to a fna file ? Or just use read1 / read2 ? Thanks for any suggestions.

Best Min

TonyaWard commented 6 years ago

Hi Min,

Thanks for using BugBase. I would recommend just using read 1.

-Tonya

On Fri, Feb 23, 2018 at 8:33 PM, chenminicode notifications@github.com wrote:

Hi, I'm trying to use paired-end shotgun reads, picking OTU with the IMG reference sequences. The command shogun_bugbase -i path_to_sequences -o output_path -u path_to_shogun_bugbase_db, -i option support fna file input, I have paired-end fastq reads, should I merge read1 and read2 to a fna file ? Or just use read1 / read2 ? Thanks for any suggestions.

Best Min

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