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Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
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What should I put in the Barcode and LinkerPrimer sequences in QIIME Mapping file ? #2139

Closed SantoshThapa1 closed 8 years ago

SantoshThapa1 commented 8 years ago

Hello,

I'm continuously having trouble of run abort while trying to analyze my MiSeq data using QIIME Visualization App available on Miseq BaseSpace. The error reads "Error in make_emperor.py: None of your sample identifiers match between the mapping file and the coordinates file. Verify you are using a coordinates file and a mapping file that belong to the same dataset."

Can anyone help me to figure me out what's wrong with my mapping file setup.

(1) BarcodeSequence: What should I put in this column ? Is it the Nextera XT 5' Index Primer sequence (such as the sequence for N724, Nxxx) or a different one?

(2) LinkerPrimerSequence: What should I put in this column ? Is it forward primer sequence (such as 515F sequence GTGCCAGCMGCCGCGGTAA that I am using for my experiments) ?

Any suggestions in this matter would be appreciated.

Thanks, Santosh

ElDeveloper commented 8 years ago

The problem you are experiencing is due to the names of your samples in your mapping file, and in your OTU table not matching. There's a file in the output of the "QIIME Preprocessing" app that has a summary of your BIOM table, look for the sample identifiers listed there, they should match one-to-one the sample identifiers (entries in the first column) of your mapping file.

On (Mar-25-16|11:02), SantoshThapa1 wrote:

Hello,

I'm continuously having trouble of run abort while trying to analyze my MiSeq data using QIIME Visualization App available on Miseq BaseSpace. The error reads "Error in make_emperor.py: None of your sample identifiers match between the mapping file and the coordinates file. Verify you are using a coordinates file and a mapping file that belong to the same dataset."

Can anyone help me to figure me out what's wrong with my mapping file setup.

(1) BarcodeSequence: What should I put in this column ? Is it the Nextera XT 5' Index Primer sequence (such as the sequence for N724, Nxxx) or a different one?

(2) LinkerPrimerSequence: What should I put in this column ? Is it forward primer sequence (such as 515F sequence GTGCCAGCMGCCGCGGTAA that I am using for my experiments) ?

Any suggestions in this matter would be appreciated.

Thanks, Santosh

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SantoshThapa1 commented 8 years ago

Thank you for your help.

genotipo commented 8 years ago

Hello I am new in qiime so I decided take qiime basespace for the analysis of my dataset. Now I ask me about the why i can't see and read nothing in paper about qiime basespace. If i sent my report is acceptable public mi paper with basespace qiime?

gregcaporaso commented 8 years ago

Hi @genotipo, The BaseSpace QIIME application is newer than the QIIME paper, which is why it's not covered in there. It's fine to publish results generated with the QIIME BaseSpace app, as BaseSpace is just wrapping QIIME. You should cite the original QIIME Nature Methods paper, as well as the relevant citation for BaseSpace if one exists. @ElDeveloper, do you know how BaseSpace itself should be cited?

genotipo commented 8 years ago

Thanks it is really good new. Only I was asking, because I am analysing my dataset now for my PhD. I was looking about the how basespace cited so I know.

2016-04-14 14:27 GMT+02:00 Greg Caporaso notifications@github.com:

Hi @genotipo https://github.com/genotipo, The BaseSpace QIIME application is newer than the QIIME paper, which is why it's not covered in there. It's fine to publish results generated with the QIIME BaseSpace app, as BaseSpace is just wrapping QIIME. You should cite the original QIIME Nature Methods paper, as well as the relevant citation for BaseSpace if one exists. @ElDeveloper https://github.com/ElDeveloper, do you know how BaseSpace itself should be cited?

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/biocore/qiime/issues/2139#issuecomment-209913691

ElDeveloper commented 8 years ago

@gregcaporaso @genotipo, to the best of my knowledge there's no citation available for BaseSpace, but I think it's fine to just link to their main website. To add to @gregcaporaso's suggestion on citing QIIME: in BaseSpace there's a few tools being used that you should cite as they are used as part of the default pipeline:

genotipo commented 8 years ago

Thanks you El 14/4/2016 19:01, "Yoshiki Vázquez Baeza" notifications@github.com escribió:

@gregcaporaso https://github.com/gregcaporaso @genotipo https://github.com/genotipo, to the best of my knowledge there's no citation available for BaseSpace, but I think it's fine to just link to their main website. To add to @gregcaporaso https://github.com/gregcaporaso's suggestion on citing QIIME: in BaseSpace there's a few tools being used that you should cite as they are used as part of the default pipeline:

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/biocore/qiime/issues/2139#issuecomment-210049438

genotipo commented 8 years ago

[image: Imágenes integradas 1] Hello, I put running my samples 2 days ago, the numbers is 245 samples. Is this normal? because this is only a sub populations, the total samples is

  1. Thanks you for your helps.

2016-04-14 14:27 GMT+02:00 Greg Caporaso notifications@github.com:

Hi @genotipo https://github.com/genotipo, The BaseSpace QIIME application is newer than the QIIME paper, which is why it's not covered in there. It's fine to publish results generated with the QIIME BaseSpace app, as BaseSpace is just wrapping QIIME. You should cite the original QIIME Nature Methods paper, as well as the relevant citation for BaseSpace if one exists. @ElDeveloper https://github.com/ElDeveloper, do you know how BaseSpace itself should be cited?

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/biocore/qiime/issues/2139#issuecomment-209913691

ElDeveloper commented 8 years ago

@genotipo, would you mind posting this question (including a little bit more information about the problem) to the QIIME forum:

https://groups.google.com/forum/#!forum/qiime-forum

genotipo commented 8 years ago

I ask in forum and nobody respond. I don't know if I need stop the analysis...

genotipo commented 8 years ago

Hello My run not finished yet, I am stressful because I connected with illumina support and they said me that ask in this forum. I tried put 10 samples, 20 samples, 30 samples, 40 samples and the run was good but when i try put 50 samples in the same time the program no finish. The problem is that in my lapton can't install qiime because isn't good lapton, it is a i3 with 4GB RAM and windows 32bits so the unique opcion is use qiime app basespace. Can Someone Help me? please