Hello, my colleague gave me some of old sequencing data (MiSeq). I have never seen the format before. My own sequencing center usually gave us three file, Forward.fastq, Reverse.fastq, Index.fastq. which are easy. The old data from other sequencing center, but split by samples. Each sample, there i…

Hello! Some sequencing facilities send already demultiplexed reads. In that case barcodes are usually removed at demultiplexed step. If the reads are in Casava 1.8 paired end demultiplexed format, barcode sequence should be indicated in the files names right after sample ID. Barcodes are needed f…

Hello! Thank you so much. "If the reads are in Casava 1.8 paired end demultiplexed format, barcode sequence should be indicated in the files names right after sample ID." Do you mean the Casava 1.8 format must have the barcode sequence on the file name? If so, I don't think I have this kind of fil…

[image] sdpapet: 210623Helob01_S100_L001_R1_001.fastq.gz 210623Helob01_S100_L001_R2_001.fastq.gz Oh, I need to apologise - I thought that barcodes in the name are the requirement, but now I see that you have different information there. [image] sdpapet: I just need to figure out if the …

Hi, thank you very much. 1> Yes, from the file name (without barcode sequence on it), the barcodes are supposed removed by the sequencing center. However, I was told these samples were sequenced using 2X250bp MiSeq. I checked the raw fastaq files, all the sequence length in the file are ~ 250bp. I…

[image] sdpapet: I checked the raw fastaq files, all the sequence length in the file are ~ 250bp. In my samples barcodes were in the F reads, so after demultiplexing it looks like this: [Screenshot from 2022-10-28 09-29-34] If the length of both F and R reads is 250, then barcodes are not …

[image] timanix: provide corresponding sequences to it “If you’re going to use DADA2 to denoise your sequences, you can remove biological sequences at the same time as you call the denoising function. All of DADA2’s denoise fuctions have some sort of --p-trim parameter you can specify to remo…

You need to provide sequences of primers to remove them. Correct [image] sdpapet: If I only leave 200 bp of F and R reads, would be safe to join them together? (I don’t want to have a lot of errors of joining) You need at least 12 nt in the overlapping region between reads to be merg…

Thank you very much! "You need to provide sequences of primers to remove them." I can provide the primers sequences, but I don't know barcodes. So, there is no way that I can provide the barcode sequences. You mentioned, "I would suggest to use cutadapt to remove forward and reverse primers that we…

[image] sdpapet: I can provide the primers sequences, but I don't know barcodes. So, there is no way that I can provide the barcode sequences. You mentioned, "I would suggest to use cutadapt to remove forward and reverse primers that were used in library preparation and discard any reads without…

QIIME 2 Forum

Can anyone help me with data from sequencing center

User Support

import

show post in topic

Home
Categories
Guidelines
Terms of Service
Privacy Policy

Powered by Discourse, best viewed with JavaScript enabled