Problema para crear un archivo manifest en Q2 studio

User Support
1

Tengo los archivos fastq, derechos y reversos, en formato comprimido, necesito crear el archivo manifiesto y no se como. Soy nueva en este tema y no tengo muchos conocimientos en programación. Aclaro que todas las secuencias están en archivos separados. Agradecería mucho su ayuda.
Laura

1 Like
2

Hi @LauMarAv,
Welcome to the forum!
I apologize for responding in English, I don’t speak Spanish but did use google translate on your original question.
Have you looked through the importing tutorial section on manifest imports? This shows you the manifest format that you need, these can be made with any regular text editor software saved in the .tsv format.

1 Like
3

Hola @Mehrbod_Estaki ,
Gracias por responder, yo no hablo ingles pero también uso google traslate.
He estado viendo los tutoriales, pero no logro crear el archivo manifest.csv y el metadata.tsv.
Por lo que me has dicho, ¿puedo hacerlo en ecxel, por ejemplo?, pero los archivos fastq son muy grandes, ¿se puede igual?
Muchas gracias por responder.
Laura

1 Like
4

Hi @LauMarAv,
Yes, you can totally use excel (or even google spreadsheet) to create your manifest file. Any text editor app will do really! Just make sure to save your manifest file as a .tsv if you are following the tutorial. This manifest file is simply used as a map to tell Qiime2 where the location of your fastq files. So it doesn’t matter how big those files are. Just make sure that the paths you provide are absolute paths.

2 Likes
5

Hi, @Mehrbod_Estaki and @LauMarAv

I’ll chip in since you reminded me of a mistake I made when I first approached Qiime2:

If you have already demultiplexed fastq.gz files with forward and reverse reads and quality scores, you might not need to create a manifest file. So, to import your raw reads, your command line might look like this:

qiime tools import \
    --type 'SampleData[PairedEndSequencesWithQuality]' \
    --input-format CasavaOneEightSingleLanePerSampleDirFmt \
    --input-path ../rawFiles/ \
    --output-path ./step.01a.demux.pe.qza

You will still need to create a tab-delimited file for your metadata.

Hope it helps.
Best,
Max

2 Likes
6

Gracias, lo voy a probar también.
Saludos
Laura

1 Like
7

Just to clarify on @mstagliamonte’s advise here, this approach only works if your fastq files follow the conventional Casava 1.8 naming format. The reason I recommended the manifest import is that it is a safer approach if you are not sure of your naming convention because it has no limitations on naming format.

4 Likes
8

Thank you, @Mehrbod_Estaki,

Now I know one more thing : :wink:

@LauMarAv : Buena Suerte :wink:

2 Likes
9

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.