Entering edit mode
9 months ago
biotrekker
▴
110
Is there a reason why fastq files from SRAExplorer and SRAToolkit are different sizes?
I am downloading paired end single-cell rna-seq data. I am getting different sizes for both SRAExplorer and SRAToolkit for the same sample's fastq.gz files. Should they not be the same size? Additionally it seems read_1 and read_2 are also switched between the methods?
Thanks
SRAExplorer is giving you links (for the data from ENA/EBI). Where as SRAtoolkit is getting the data from NCBI/SRA.
It is possible that the reads are getting switched so check then files carefully. Post the SRA# if you want someone else to check.
I would appreciate it: GSE157827 with SRP number below: SRP282056
There are many SRR accessions in this project. I tried one from both SRA and links from SRA-toolkit. Both downloads were in right order.
From SRA-Explorer
where they the same size? As in between SRA toolkit and SRA explorer?
I did not download the full dataset. Question you had was about the possibility of switching of the reads among the two methods. Answer for that is no.