Hi, I have got fastq.gz samples from my sequencing provider after spilt libraries and demultuplexing. In this run, I had 6 samples and he sent me 6 forward file and 6 reverse files separately. I used to work with Qiime 1.... a lot and now I wish to try Qiime 2. I have several Q: Do I need to c…

[image] Nir_Friedman: Do I need to combine all the 6 forward files into one combined file and all the 6 reverse files into another file in order to start the analysis? No! If your reads are already demultiplexed you can use the manifest format to import these. However, you mention "split li…

Thanks Nicholas. My seq provider did not use qiime for sure, he uses Qiagen's CLC. According to him the used split libraries ( maybe he mistakenly used this term, when he actually meant for demultiplexing the samples). The output that I have got is 12 files, 6 forward (R1) , 6 revers (R2) fastq.g…

[image] Nir_Friedman: My seq provider did not use qiime for sure, he uses Qiagen’s CLC. According to him the used split libraries ( maybe he mistakenly used this term, when he actually meant for demultiplexing the samples). Thanks for clarifying! That's good — some sequence providers use qii…

Excellent. Thanks a lot. Will try it and get back to you if needed. Nir

Hi Nicholas, Your answer was very helpful and i manged to upload the files. I then ran this command to clean non biological sequences. qiime dada2 denoise-paired --i-demultiplexed-seqs /home/qiime2/Desktop/Netanya_6/paired-end-demux.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 240 …

Hi @Nir_Friedman , Here is the key line: [image] Nir_Friedman: Memory allocation failed. You do not have enough memory to run this command! You will probably need to find a more powerful machine to run this (usually 8 GB RAM should suffice for a dada2 with a single sequencing run, but the mo…

Hi Nicholas, I have designated 4 GB RAM and 3 CPUs ( my laptop has 32 GB RAM and 8 CPUs) Should I increase only the RAM or also the CPUs? Was this the only problem? ( just to rerun the command?) Tx Nir

[image] Nir_Friedman: I have designated 4 GB RAM and 3 CPUs ( my laptop has 32 GB RAM and 8 CPUs) Should I increase only the RAM or also the CPUs? Increase RAM. No need to increase CPUs unless if you want to. [image] Nir_Friedman: Was this the only problem? ( just to rerun the command?) …

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Importing fastq files after demultiplexing

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