will produce three files, with the first being the index file (you don't need that), the second one the UMI+CB and the third one the cDNA read. I would include --gzip to compress the files right away. Usually I would also use prefetch to download the sra file first and then run fastq-dump on that file for the conversion as the latter tool is notoriously unstable and unreliable, hence running on the downloaded file is usually a bit more robust. Typically I recommend visiting sra-explorer.info to get fastq download links directly but recently it seems to be non-functional, maybe due to changes in the ENA API that it queries for download links, at least it does not return anything in my hands so using prefetch+fastq-dump is the choice I guess.
I did the prefetch command to download sra filed and then did ~/sra_data/SRR19687957$ fasterq-dump SRR19687957 --split-files
I also had my coworker try the way he normally does and he says he also is only getting one file instead of 2; he used fastq-dump command
If you prefetch first then it is fastq-dump (...) SRR19687957.sra on the downloaded file. Otherwise it makes no sense. Why fasterq again, I think it was demonstrated here compellingly that this is no choice.
This sra contains three fastq files. I1, R1 and R2 as mentioned in metadata. fastq-dump with --split-files should works. Can you paste your command here?
Yeah, another brick in the wall why fasterq-dumb (b is not a typo) is even worse than the original version, unable to perform basic operations and not providing gzip compression options. Absolutely terrible, like the enrire SRA framework. This entire sra2fastq conversion thing is one of the top unnecessary wastes of computation resources.
I've demonstrated fastq-dump is the only option. Should you try the suggested script first? I don't know what command your coworker used so I'm not going to comment on this.
-O refers to the output directory. You can check all arguments with --help.
You should add surfix .sra to the downloaded file. Otherwise, it will automatically download the data from SRA no matter you have downloaded it or not. The output directory need to be a different path to be distinguished from the directory which contains your downloaded .sra files. I tested many times to make fastq-dump/fasterq-dump work, it always report error when I stored the sra files with splited fastqs.
I tried both ways .sra and without .sra, both which correctly produced 3 files _1/2/3.fastq.gz
The number of read and written spots match up as well for the one without .sra.
side note: coworker's command was fasterq-dump --split-files SRR19687957.sra -- gzip which he said it still gave output as one read file. He tried it with a completely different accession number which he got 2 running the same command, but he said for some reason this one that Im working on only gave out one.
I did the prefetch command to download sra filed and then did ~/sra_data/SRR19687957$ fasterq-dump SRR19687957 --split-files I also had my coworker try the way he normally does and he says he also is only getting one file instead of 2; he used fastq-dump command
If you prefetch first then it is
fastq-dump (...) SRR19687957.sraon the downloaded file. Otherwise it makes no sense. Why fasterq again, I think it was demonstrated here compellingly that this is no choice.Got-it, I'll just stick with fastq-dump command when splitting files. Thanks for the explanation and help!