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benjjneb
Issues with assigning identical(colnames(ASVs),rownames(taxa))
Please can anyone tell me why i kept on getting FALSE for this command identical(colnames(ASVs),rownames(taxa)). identical(colnames(ASVs),rownames(taxa))i tried checking the ASV counts and Taxonomy counts, they are both the same number but it is still giving me FALSE. I also change the command to col and row but all efforts prove abortive. Thanks for your support
You haven't provided enough information here to diagnose your problem. Are you... following the DADA2 tutorial? Where are you in it? Are things working previously? What are the dim(ASVs) and dim(taxa)?
Thank you so much for responding, I am highly frustrated right now. I am using DADA2 to analyze my data. I have finished running DADA2 (aligning my sample to reference genome RDP and Silver and saving in .RDS format). I have also been able to import my output into R studio but the issue is the ASVs count generated is not the same as my taxonomy count although both have the same dimensions. This brings the error and I cant proceed.
Eagerly waiting for your assistance, Thanks
Warm regards, Abiola
On Tue, Jul 12, 2022 at 10:27 PM Benjamin Callahan @.***> wrote:
You haven't provided enough information here to diagnose your problem. Are you... following the DADA2 tutorial? Where are you in it? Are things working previously? What are the dim(ASVs) and dim(taxa)?
— Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1583#issuecomment-1182469978, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWB5E72AJR7NORHSIJIO36DVTXIKRANCNFSM53GVRFKQ . You are receiving this because you authored the thread.Message ID: @.***>
This doesn't help, your comments are not giving enough information to identify the issue you are having. You have "finished running DADA2" -- how? By following the DADA2 tutorial? And, did you get something sensible at the end? How did you save the RDS objects?
In order to get useful support what you are doing needs to be clearly defined. One way to start might be to start over using just two samples from your dataset, run through the DADA2 tutorial, then report the read tracking numbers at the end.
Yes, I have finished running DADA2, I followed the tutorial. I think I did get a good result and saved it as RDS. Please find attached some of My results, you can advise further.
On Tue, Jul 12, 2022 at 11:25 PM Benjamin Callahan @.***> wrote:
This doesn't help, your comments are not giving enough information to identify the issue you are having. You have "finished running DADA2" -- how? By following the DADA2 tutorial? And, did you get something sensible at the end? How did you save the RDS objects?
In order to get useful support what you are doing needs to be clearly defined. One way to start might be to start over using just two samples from your dataset, run through the DADA2 tutorial, then report the read tracking numbers at the end.
— Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1583#issuecomment-1182514517, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWB5E77TBG46RKTBR2TNQMTVTXPEDANCNFSM53GVRFKQ . You are receiving this because you authored the thread.Message ID: @.***>
I am currently rerunning the DADA2 script. Are there different script for DADA2? maybe you can send me your script. How can I solve the problem of reorientation? could this be from when I am demultiplexing, removing primers and barcode using FASTQProcessor?
Thank you for your help, I am indeed grateful.
Sincerely, Abiola
On Wed, Jul 13, 2022 at 12:18 AM abdulsalam rukaiyat @.***> wrote:
Yes, I have finished running DADA2, I followed the tutorial. I think I did get a good result and saved it as RDS. Please find attached some of My results, you can advise further.
On Tue, Jul 12, 2022 at 11:25 PM Benjamin Callahan < @.***> wrote:
This doesn't help, your comments are not giving enough information to identify the issue you are having. You have "finished running DADA2" -- how? By following the DADA2 tutorial? And, did you get something sensible at the end? How did you save the RDS objects?
In order to get useful support what you are doing needs to be clearly defined. One way to start might be to start over using just two samples from your dataset, run through the DADA2 tutorial, then report the read tracking numbers at the end.
— Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1583#issuecomment-1182514517, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWB5E77TBG46RKTBR2TNQMTVTXPEDANCNFSM53GVRFKQ . You are receiving this because you authored the thread.Message ID: @.***>
Yes, I have finished running DADA2, I followed the tutorial. I think I did get a good result and saved it as RDS.
We know, from this thread and your other thread, that the result you have at the end is not correct. The goal now is to diagnose where the workflow went wrong.
Could this be from when I am demultiplexing, removing primers and barcode using FASTQProcessor?
It could be, but it could be from other things.
What I recommend is to subset your data down to 2 samples. Then run through the DADA2 tutorial workflow, and start by reporting the read tracking numbers: https://benjjneb.github.io/dada2/tutorial.html#track-reads-through-the-pipeline
That will help a lot in identifying where the workflow is going wrong.
Good morning, Thank you for the assistance, I got relieved when you assist. I am running for two samples as suggested by you, calculating the error rate is taking forever but as soon as I finish, will track the read number and send the results to you. Thank you so much.
Warm regards, Abiola
On Wed, Jul 13, 2022 at 1:12 AM Benjamin Callahan @.***> wrote:
Yes, I have finished running DADA2, I followed the tutorial. I think I did get a good result and saved it as RDS.
We know, from this thread and your other thread, that the result you have at the end is not correct. The goal now is to diagnose where the workflow went wrong.
Could this be from when I am demultiplexing, removing primers and barcode using FASTQProcessor?
It could be, but it could be from other things.
What I recommend is to subset your data down to 2 samples. Then run through the DADA2 tutorial workflow, and start by reporting the read tracking numbers: https://benjjneb.github.io/dada2/tutorial.html#track-reads-through-the-pipeline
That will help a lot in identifying where the workflow is going wrong.
— Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1583#issuecomment-1182586304, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWB5E77C2NQ3B6KU3TQUGL3VTX3WTANCNFSM53GVRFKQ . You are receiving this because you authored the thread.Message ID: @.***>
The error rate for forward reads is still running since morning, can I terminate it and rerun or does it take this long. I am only running for two samples as directed by you. Thank you so much for your response.
Sincerely, Abiola
On Wed, Jul 13, 2022 at 10:45 AM abdulsalam rukaiyat @.***> wrote:
Good morning, Thank you for the assistance, I got relieved when you assist. I am running for two samples as suggested by you, calculating the error rate is taking forever but as soon as I finish, will track the read number and send the results to you. Thank you so much.
Warm regards, Abiola
On Wed, Jul 13, 2022 at 1:12 AM Benjamin Callahan < @.***> wrote:
Yes, I have finished running DADA2, I followed the tutorial. I think I did get a good result and saved it as RDS.
We know, from this thread and your other thread, that the result you have at the end is not correct. The goal now is to diagnose where the workflow went wrong.
Could this be from when I am demultiplexing, removing primers and barcode using FASTQProcessor?
It could be, but it could be from other things.
What I recommend is to subset your data down to 2 samples. Then run through the DADA2 tutorial workflow, and start by reporting the read tracking numbers: https://benjjneb.github.io/dada2/tutorial.html#track-reads-through-the-pipeline
That will help a lot in identifying where the workflow is going wrong.
— Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1583#issuecomment-1182586304, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWB5E77C2NQ3B6KU3TQUGL3VTX3WTANCNFSM53GVRFKQ . You are receiving this because you authored the thread.Message ID: @.***>
Good evening Doc., Sequel to our discussion, please find attached, my results for two sample run. Thank you for your assistance.
Sincerely, Abiola
On Wed, Jul 13, 2022 at 1:12 AM Benjamin Callahan @.***> wrote:
Yes, I have finished running DADA2, I followed the tutorial. I think I did get a good result and saved it as RDS.
We know, from this thread and your other thread, that the result you have at the end is not correct. The goal now is to diagnose where the workflow went wrong.
Could this be from when I am demultiplexing, removing primers and barcode using FASTQProcessor?
It could be, but it could be from other things.
What I recommend is to subset your data down to 2 samples. Then run through the DADA2 tutorial workflow, and start by reporting the read tracking numbers: https://benjjneb.github.io/dada2/tutorial.html#track-reads-through-the-pipeline
That will help a lot in identifying where the workflow is going wrong.
— Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1583#issuecomment-1182586304, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWB5E77C2NQ3B6KU3TQUGL3VTX3WTANCNFSM53GVRFKQ . You are receiving this because you authored the thread.Message ID: @.***>
Good day, You are not responding to my email. Please kindly respond so that I can meet up with the deadline. Please
Thanks Abiola
On Wed, Jul 13, 2022 at 10:22 PM abdulsalam rukaiyat @.***> wrote:
Good evening Doc., Sequel to our discussion, please find attached, my results for two sample run. Thank you for your assistance.
Sincerely, Abiola
On Wed, Jul 13, 2022 at 1:12 AM Benjamin Callahan < @.***> wrote:
Yes, I have finished running DADA2, I followed the tutorial. I think I did get a good result and saved it as RDS.
We know, from this thread and your other thread, that the result you have at the end is not correct. The goal now is to diagnose where the workflow went wrong.
Could this be from when I am demultiplexing, removing primers and barcode using FASTQProcessor?
It could be, but it could be from other things.
What I recommend is to subset your data down to 2 samples. Then run through the DADA2 tutorial workflow, and start by reporting the read tracking numbers: https://benjjneb.github.io/dada2/tutorial.html#track-reads-through-the-pipeline
That will help a lot in identifying where the workflow is going wrong.
— Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1583#issuecomment-1182586304, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWB5E77C2NQ3B6KU3TQUGL3VTX3WTANCNFSM53GVRFKQ . You are receiving this because you authored the thread.Message ID: @.***>
Sequel to our discussion, please find attached, my results for two sample run.
I don't see anything attached to your post. I don't think it is possible to attach large files to GH comments.
Can you paste in the results of the read-tracking section of the tutorial workflow for these two samples?
Good evening, After Tracking reads input Filtered denoisedF denoisedR Merged nonchem Sample 1 1225431 1098159 1092853 1091220 1038421 625513 Sample2 1023850 899510 896644 896552 859530 517453
On Thu, Jul 14, 2022 at 7:13 PM Benjamin Callahan @.***> wrote:
Sequel to our discussion, please find attached, my results for two sample run.
I don't see anything attached to your post. I don't think it is possible to attach large files to GH comments.
Can you paste in the results of the read-tracking section of the tutorial workflow for these two samples?
— Reply to this email directly, view it on GitHub https://github.com/benjjneb/dada2/issues/1583#issuecomment-1184695991, or unsubscribe https://github.com/notifications/unsubscribe-auth/AWB5E75S7XD4H5VCSIU43SLVUBDDXANCNFSM53GVRFKQ . You are receiving this because you authored the thread.Message ID: @.***>
Edit: Misread the column headings. Most reads are being lost at the chimera stage. This issue seems a duplicate of #1582 so please direct discussion there.