I installed qiime 2 within miniconda. Attached a picture of the FASTQ file I found in my lab. I can not find any identifier for forward or reverse read or sample ID. How to use data in this file to do manifest file? alternative way, if I downloaded FASTQ from basespace website, how to import this file into qiime to make the manifest file? Thanks a lot
Hi HebaHussein-1981, Do you have single end reads? -That is what I can assume from your column here. If so, then for all your samples, you need to prepare a manifest file like the one below. This can be done using a spreadsheet and then saving the file in tab delimited format.
(Regarding your sample id it would be upto you how you would name it)
Then you should import the fastq.gz files using the commands ( SingleEndFastqManifestPhred33V2)
I don’t have any experience with using the miniconda environment, but is there a way in which you could upload your sequences as well as the manifest file to the terminal? If so, then after uploading the sequences & manifest file, you need to follow the commands on the importing data tutorial.
Thanks my issue is I do not know how to prepare manifest file. Shall i copy and paste manually sample IDs from FASTQ file? then how to know reverse and forward read? if it is single read, how to know if it is forward or reverse?
Yes you can manually copy-paste your sample ids from the fastq file. Usually, in my samples, when i have both the forward reads and reverse reads, the sample name would be same except that they would have R1 and R2 in sample names/id: which would indicate R1 to be the forward read and R2 the reverse read. So in your fastq file you should check to see if you have R1 and/or R2. Example: if forward read is AB_001_R1.gz then the reverse read would be AB_001_R2.gz.
Incase of single read how naming is done depends on the sequencing company. But in order to identify whether you have forward or reverse read, you can do the following:
First use your forward primer to check if the sequence in your fastq file has this primer. Then it would be easier to conclude that the read you have is the forward read.
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