I got pair-end fastq files from Miseq, 2X300bp to cover V1-V2 region, these samples have been demultiplexed with barcode removed, i.e. each sample has R1 R2 fastq files with v1 primer and reverse v2 primer, but no barcode inside. How can I import these fastq file without demultiplex again in Qiime2…

Hi @L_Zh ! I am not 100% following what you have outlined here, so my apologies if I misunderstood! If your primers are on the 5' end of the input sequences, and are all the same length, you can use the --p-trim-left-f/--p-trim-left-r flags to strip the primers out. Otherwise, it sounds like pre-pro…

Thanks thermokarst: In my demultiplexed data got from Miseq, we use 27F as v1 primer, and part of 341F as v2 primer. We designed as 2X300bp, but when we got data, the read length varied because the quality cutoff e.g in R1 (removed Quality line) Bold is revise primer for V2: @M00800:84:000000000…

Hey @L_Zh , [image] L_Zh: the read length varied So the sequencing core is performing some sort of quality filtering and trimming prior to handing you the data? [image] L_Zh: Bold is revise primer for V2 Based on that R1 sequence, it looks like the issue is that you have some reverse …

Thanks Nicholas Since the data i got have various bp length reads due to the quality cut. I have asked the raw bcl file from Miseq, do you know how can I generate Qiime2 format fastq file from the bcl raw data?

Hi @L_Zh , Your sequence center would probably have a better idea about processing bcl files — but I don't think that will even be necessary. I think I have a better idea of your original question now — you can still use cutadapt to trim primers form your reads, then import as described here . No joi…

QIIME 2 Forum

How to process pair-end demultiplexed seq with qiime2

User Support

dada2, import

show post in topic

Home
Categories
Guidelines
Terms of Service
Privacy Policy

Powered by Discourse, best viewed with JavaScript enabled