ENA fastq file shown as single-end but has 2 fastq files: X.fastq.gz and Y.fastq.gz

Question

[Aaliya]

Hello, I am downloading some data from this project from ENA: https://www.ebi.ac.uk/ena/browser/view/SRX13384934

It is mentioned that the data is single ended, but there are still two fastq files (their experimental accession number is the same).

I tried to confirm this on NCBI SRA as well: https://www.ncbi.nlm.nih.gov/sra/?term=SRX13384934 Even on NCBI SRA, it is mentioned that it is single end, but there are two fastq files given.

I am assuming that the two files are the same and the number of runs which were done for this sample set was two for confirmation?

I have done fastqc and trimmomatic on these files, and they do differ by sequence length, should I opt for the one best in quality?

I have to take either of these files to perform Kallisto and then DESeq2.

Thank you in advance!

Answer 1

[swbarnes2]

It's probably the same library run twice, I which case, trim the longer on to be the same length as the shorter, then use both.

[Aaliya]

I cannot use both, to perform Kallisto quantification I need one single file only.

[GenoMax]

@swbarnes is correct. If you look at the data access tab for these entries in SRA ( one example https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR17204972&display=data-access ) then you will see that there are L001 and L002 in the original file names. This means the same sample was run on two lanes.

You can cat file1.gz file2.gz > one_file.gz and use the single file as input.

Both samples were run as 75 bp. You will get a range of read length after trimming the data. That is normal.

[Aaliya]

I understood what you are implying, thank you