Although I use QIIME 2, I need to import my data in Qiime 1.9 to check something. but I cannot find any tips or tutorial for importing some demultiplexed paired-end fastq files with quality score. I just need to determine how many read my samples have.
could you please give me a link or something for that?
If you just need the number of reads your samples has I would recommend sticking with QIIME 2, using the
qiime demux summarize command. If you absolutely need to go into QIIME 1 for some other reason, you can export your data from Q2, (see exporting tutorial here) and use them in Q1 as you normally would.
Thank you for your information.
it is necessary to work with qiime 1 actually but I prefer to start with Qiime 1 with no Intervention of qiime2.
I need to compare something in both qiime 1 and qiime 2 as my lecturer asked me.
is there any command to show just the sample reads? or to import data in qiime 1 then visualize it like qiime 2?
Ok, sounds like you just need QIIME 1 support without the Q2 involvement.
I’m not all that familiar with QIIME 1, but from a quick search through their scripts list, looks like you want the count_seqs.py command.
On another note, I should mention that comparing QIIME 1 to QIIME 2 is not something I would personally recommend, mainly because these are wrappers for hundreds of other scripts and tools, so no matter what you do you can’t really say “this worked better than that”. Your efforts are better put towards comparing the underlying methods used in each, and with that mentality there are very few things in QIIME 1 that you can’t also do in QIIME 2.
Anyways, good luck!
Thank you very much.
Honestly the reads of my samples are too low while my lecturer said they were much more in qiime1 already. So she asked me to try the data in qiime1 and see the reads. This is the main issue.
Do you think is it possible to have different reads in qiime 1 and qiime 2?
If you have demultiplexed fastq files and you just want to count the number of reads in each sample, you shouldn’t find any differences between QIIME 1 and 2, since you are not doing anything to modify these files, you’re simply just tallying them. But if you had performed some sort of processing first, for example, demultiplexing, trimming primers, denoising/OTU picking etc. then yes it is likely you would see some differences, again not because one is QIIME 1 and QIIME 2, but because of the underlying tools being wrapped by QIIME.
no, I didn’t do anything with the data. it’s already demultiplexed.
Ok. Thank you for your all help Dear Mehrbod.
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