Hello colleagues I am new to QIIME2. I had illumina R1 and R2 files I applied extract_barcodes.py in Qiime1 to get Reads1.fastq , Reads2.fastq and Barcodes.fastq I converted them all to individual .gz files and then imported them using qiime tools import --type EMPPairedEndSequences --inpu…

Dear @benjjneb Dear @thermokarst yes I was doing V4 region sequence analysis with 515F 806R primers. --p-trunc-len-f 220 --p-trunc-len-r 220 served the job. Feeling obliged sir

Hello Dear Colleague I am still confused regarding importing data. Can you help me to construct the command In the shared folder I have three files as an output of extract_barcodes.py in the "processed_seqs" folder Barcodes.FASTQ Reads1.FASTQ Reads2.FASTQ First I define the path of Qiime2 to…

Hi @drmusk , thanks for writing! It looks like your import went well, and the results from running demux summarize appear reasonable at first glance: [23 PM] Have you made sure your Chrome or Firefox installations are up to date? You could share a screenshot of the error page you see when loading…

Dear Dr Dillon Sorry, I will be cautious next time while posting. Thanks for suggesting $ qiime tools view MY_VIZ.qzv It helped. I ran this command again with --verbose and got a big message which is attached herewith dada2 error message.txt (5.9 KB) qiime dada2 denoise-paired --i-demultiplexed…

[image] drmusk: Input must be a valid sequence table Hi @drmusk , thanks for posting the error message. @benjjneb , I wonder if this is related to this bug on the DADA2 issue tracker ?

I suspect this one is due to none of the sequences being succesfully merged (hence the sequence table is empty and not "valid"). @drmusk can you clarify the primer set you are using? Is it the ~252 nucleotide V4 amplicon region? If it is, when the reads are truncated to 120/120, they won't overlap …

QIIME 2 Forum

Qiime dada2 denoise-paired end sequences

User Support

dada2, q2view

show post in topic

Home
Categories
Guidelines
Terms of Service
Privacy Policy

Powered by Discourse, best viewed with JavaScript enabled