Hi @jennaj
Thanks for the information. I checked on the format for reads that worked or not:
- for 55 (which worked) “uploaded fastqsanger.gz file”
- for 44 (which did not work) “uploaded fastq.gz file”
So one is fastq and one is fastqsanger but both seems to be compressed, as per .gz
My understanding is that on Galaxy, an uncompressed file was created for entry 55 using the fastqsanger. gz file, but that could not be done using a fastq.gz file?
I’m not too sure to understand your comment on FastQC. I actually ran FastQC on all my data as well as multiQC, which seemed to show good results, and then I ran Trimmomatic an all reads. The trimmimg seems to also have worked, and I tried to run Unicycler first using the trimmed reads instead of raw data, but this did not work.
Summary results from FastQC for 44 is:
#fastqc 0.11.8
Basic Statistics pass
#Measure Value
Filename 6461x11601MD-SKQ_S1_L001_R1_001_fastq_gz.gz
File type Conventional base calls
Encoding Sanger / Illumina 1.9
Total Sequences 856011
Sequences flagged as poor quality 0
Sequence length 35-301
%GC 31
END_MODULE
So I do not see any problem here? How does this relate to my problem?
So if I summarize, your advice is to unzip the .gz files before uploading them in order to save some space? And then, when uploading them, use the “auto” for the file format attribution?
One last thing: I should probably delete everything and upload everything again so that I start clean. If I click on the little cross on the right panel in the history, will that actually clear the space in my account? I would not want to have data in the background still using some memory.
Thanks for help
Vanina