Is there a reason why fastq files from SRAExplorer and SRAToolkit are different sizes?

Question

[biotrekker]

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

[GenoMax]

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.

[biotrekker]

I would appreciate it: GSE157827 with SRP number below: SRP282056

[GenoMax]

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.

$ head -4 SRR12623957*.fastq
==> SRR12623957_1.fastq <==
@1
GTTNGTGGTCATGGCCGCGTATTCCT
+1
FFF#FFFFFFFFFFFFFFFFFFFFFF

==> SRR12623957_2.fastq <==
@1
ATAATTTATGCCAAAGTAGTGATTCTCTTGTAAGCTATGTTCAGGTGGTCAAGATAAAAATGACATTCCTAGCAACATGGTCCTACATTAAATTATTC
+1
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

From SRA-Explorer

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR126/057/SRR12623957/SRR12623957_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR126/057/SRR12623957/SRR12623957_2.fastq.gz

$ zmore SRR12623957_1.fastq.gz

@SRR12623957.1 1/1
GTTNGTGGTCATGGCCGCGTATTCCT
+
FFF#FFFFFFFFFFFFFFFFFFFFFF
@SRR12623957.2 2/1
GTTNCGATCATTGGTGATCCATGCGC
+
FFF#FFFFFFFFFFFFFFFFFFFFFF

$ zmore SRR12623957_2.fastq.gz

@SRR12623957.1 1/2
ATAATTTATGCCAAAGTAGTGATTCTCTTGTAAGCTATGTTCAGGTGGTCAAGATAAAAATGACATTCCTAGCAACATGGTCCTACATTAAATTATTC
+
FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF
@SRR12623957.2 2/2
CCAAAGGAAAGAGCACAATGAAACGTTTGGGGGTGATGTATATATTCATTATTTGATTATGTCTAATGATTTCATGGGTGTATACATATGTCAAAACT
+
FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF

[biotrekker]

where they the same size? As in between SRA toolkit and SRA explorer?

[GenoMax]

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.