dada2
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benjjneb
getting such merged and nonchim results.
hi I am getting these results, but I am not sure whether I am doing correctly or not. are the merged and nonchim fine like i am getting results less numbers. can someone please explain me. input filtered denoisedF denoisedR merged nonchim 10002S91 30364 24809 24675 24753 2 2 10003S32 43810 34515 34273 34414 0 0 10017S79 48933 40907 40557 40663 31 31 10023S44 42875 34968 34584 34802 6 6 10028S57 42237 34366 34038 34098 29 29 10070S83 44319 36770 36232 36427 45 45
Hi, in my asv file I am getting too much NA values, I tried all the options mentioned in the tutorial but the results is same. Can you please assist me how to solve this issue.
You are losing all your reads at the merging step. This is almost always because in your filtering/trimming step, the reads were cut too short, thus they now don't overlap.
How long is your sequenced amplicon? What truncation lengths did you use? Your truncation lengths should sum up to at least 20 more than the maximum length (accounting for possible biological length variation) of the sequenced amplicon.
You are losing all your reads at the merging step. This is almost always because in your filtering/trimming step, the reads were cut too short, thus they now don't overlap.
How long is your sequenced amplicon? What truncation lengths did you use? Your truncation lengths should sum up to at least 20 more than the maximum length (accounting for possible biological length variation) of the sequenced amplicon.
hi, thank you very much for the reply you were right I was losing reads after truncation. I am working on the V1-V3 region.
Hello, I am facing problem in creating phyloseq object can you please help me. For example the name of my sample files is 102_S12_L001_R1_001, i have only this much details. And I also don't have mock data, how to follow that code please guide me.
Thanks and regards Komal Chaurasia
On Tue, 5 Apr 2022, 22:25 Benjamin Callahan, @.***> wrote:
You are losing all your reads at the merging step. This is almost always because in your filtering/trimming step, the reads were cut too short, thus they now don't overlap.
How long is your sequenced amplicon? What truncation lengths did you use? Your truncation lengths should sum up to at least 20 more than the maximum length (accounting for possible biological length variation) of the sequenced amplicon.
— Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1525#issuecomment-1089371645, or unsubscribe https://github.com/notifications/unsubscribe-auth/AYOPPXLKLSJ2L4B2C4LW2MLVDSVUBANCNFSM5SRCS2EA . You are receiving this because you authored the thread.Message ID: @.***>
@komalchrs This isn't enough information to be able to help. You'll have to be more precise about your problem, probably including what commands aren't working and what the error messages are.