Hi all,
I received paired end fastq files of casava (R1 and R2) from illumina but not barcode file. Now i have fastq files of R1 and R2 as well as metadata file. I am not sure either my reads are already demultiplexed or i have to do it before importing them into qiime2.
Here is a look of fastq file. Could you please have a look at it and let me know whether or not it contains barcodes or they are already demultiplexed.
Regards
Muhammad
Hi!
If you have only two files, one forward and one reverse, and they are quite big in size when gzipped (more than 10 mb each), that's mean that your reads are multiplexed. If you have numerous files, named as your samples in a metadata file, and each of them up to one or several mb in size, that's mean that they are already demultiplexed.
Hi timanix,
Sorry, I could not understand you properly. I have total 63 samples and for each sample i have a zip file which includes R1 and R2 files. Each zip file size is more than 15 mb.
when i open my fastq files, there are two index sequences in the header. Should i remove them before importing data in QIIME?
When i check reads quality in qiime2, the minimum sequence length comes 35 bases. I think it should not be a case as my reads have more than 250 bases.
Looks like your reads are already demultiplexed. Since you already imported those files successfully, you can proceed to work with them.
Thank you for your kind time.
Muhammad
One thing i want to share, when i checked quality of my reads, the minimum sequence length was found 35 bases in forward and reverse reads. Is this a normal case or something wrong in my sequences?
I think one can expect to have too short reads in the pool of sequences. All sequences that are shorter than truncation parameter will be discarded at the filtering step (in your second post, at Dada2 step you lost about 10% of the reads at filtering step).
It seems, the process i am doing is fine except merging. I ahve to optimize the merging process.
Would it be possible that i can denoise my data througfh deblur? is there any difference between dada2 and deblur and would it make a difference?
Yes, it is an option. But you will need to merge your reads first.
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