Is there a reason why fastq files from SRAExplorer and SRAToolkit are different sizes?
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
• 1,553 views
•
link
updated
by
GenoMax
•
written
by
biotrekker •
•
written
by
biotrekker •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Downloading paired end fastq data from SRA
written by Matheus •
-
ENA fastq file shown as Paired-end but has 2 Run Accessions
written by Aaliya •
-
How do I use md5sum to check if my .fastq files from SRA Explorer have been downloaded correctly
written by biotrekker •
-
Cell Cycle Labeled Fastq files
written by halimaakhter014 •
-
Error with fastq file corruption when downloading from SRA explorer using SLURM job
written by biotrekker •
-
BD Rhapsody single cell RNA: usable sequence
written by Darked89
-
Read groups in RNA-seq
written by Petesview •
-
Can you concatenate fastq.gz (zipped) and fastq (non-zipped) files?
written by Eliveri •
-
Prinseq lite data preprocessing
written by Adarsh Kuamr •
-
do paired end reads both mapped to the same gene appear consecutive to each other in SAM file (usin…
written by Moses
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.