Hi fellow qiime2 users,
So, i'm having this small issue in which my fastq-files names come out different from what is in the manifest file. Example
Manifest file (I replaced part of the path with
... to make it a bit more readable):
sample-id,absolute-filepath,direction 2020.10.Rotavirus.S0001,/hpc/.../demultiplexed_renamed/2020.10.Rotavirus.S0001_S1_L001_R1_001.fastq.gz,forward 2020.10.Rotavirus.S0001,/hpc/.../demultiplexed_renamed/2020.10.Rotavirus.S0001_S1_L001_R2_001.fastq.gz,reverse 2020.10.Rotavirus.S0002,/hpc/.../demultiplexed_renamed/2020.10.Rotavirus.S0002_S2_L001_R1_001.fastq.gz,forward 2020.10.Rotavirus.S0002,/hpc/.../demultiplexed_renamed/2020.10.Rotavirus.S0002_S2_L001_R2_001.fastq.gz,reverse
File names after
qiime tools export:
2020.10.Rotavirus.S0001_0_L001_R1_001.fastq.gz 2020.10.Rotavirus.S0001_1_L001_R2_001.fastq.gz 2020.10.Rotavirus.S0002_2_L001_R1_001.fastq.gz 2020.10.Rotavirus.S0002_3_L001_R2_001.fastq.gz
So, basically the 'S' number is changed to an increasing number starting from 0 for the first file and up to the amount of files exported...Now, I wouldn't really mind if this number would be the same for the R1 AND R2 files of a particular sample. So, if the '0' was there for the R2 of sample S0001 as well, for example. But it doesn't seem right to have different labels for the forward and reverse fastq-files of the same sample.
Now, I see in your documents here that you use a slightly different manifest format. On the other hand the MANIFEST that is generated by Qiime2 after exporting has the same format as my manifest-file:
sample-id,filename,direction 2020.10.Rotavirus.S0001,2020.10.Rotavirus.S0001_0_L001_R1_001.fastq.gz,forward 2020.10.Rotavirus.S0001,2020.10.Rotavirus.S0001_1_L001_R2_001.fastq.gz,reverse 2020.10.Rotavirus.S0002,2020.10.Rotavirus.S0002_2_L001_R1_001.fastq.gz,forward 2020.10.Rotavirus.S0002,2020.10.Rotavirus.S0002_3_L001_R2_001.fastq.gz,reverse
Is the difference in manifest format the reason for this "renaming"? I don't think that's supposed to be it, since I thought this other format would be only compatible with
PairedEndFastqManifestPhred33V2 and I'm using
PairedEndFastqManifestPhred33 (the non-V2 parameter). I'm also not entirely sure if it's going wrong during import or export. On the bright side, it doesn't seem to have any negative effect on the rest of the analyses, which I thought it might at first. So, it's not a huge issue, but still a bit annoying.