rvalieris
commented
2 years ago hello,
the filenames are created by the regular fastq-dump (parallel-fastq-dump uses fastq-dump directly).
looking at the run selector for this project: https://trace.ncbi.nlm.nih.gov/Traces/study/?acc=phs001839
to me, it looks like these are library replicates, and the 75x is the run coverage, you can click on the SRR links and see the run coverage number matches, I don't know what the second number is, but I think its just to make each file distinct. I'm guessing that these numbers were added to differentiate each replicate.
SRR10005214: 75x SRR10109399: 72x SRR10109400: 72x SRR10109401: 74x
the only way to be sure is to either find a paper from the original authors using this data or contact the authors directly.
Hi dbGaP,
I'm writing to ask about this specific project by NYGC: '3 CANCER CELL LINES ON 2 SEQUENCERS' dbGaP accession number: phs001839.v1.p1 https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001839.v1.p1
I've reached out to NYGC for comment on what the 72x, 74x, or 75x means or what the 48,49,45,43 means in these files: HCC1143-N_72x_48_1.fastq.gz HCC1143-N_72x_48_2.fastq.gz HCC1143-N_72x_49_1.fastq.gz HCC1143-N_72x_49_2.fastq.gz HCC1143-N_74x_45_1.fastq.gz HCC1143-N_74x_45_2.fastq.gz HCC1143-N_75x_43_1.fastq.gz HCC1143-N_75x_43_2.fastq.gz
To get these files, I had to install Aspera Connect, and then use prefetch from the SRAtoolkit and then parallel-fastq-dump to extract and gzip fastq files.
NYGC said dbGaP named these files because they uploaded these BAM files and they were converted by dbGaP to FASTQs to host on the dbGaP FTP.
dbGaP is now saying that parallel-fastq-dump named these files.
Can you help me understand how files are named in the output of parallel-fastq-dump please?
Appreciate your prompt reply and thank you!
Best, Nicole