Hi Everyone I am working on Sra files. I need to convert them into Fastq files. When i used fastq-dump on my SRR786.sra file , it gave me three files namely SRR7861.fastq, SRR7862.fastq and SRR786.fastq. I read the documentation for SRA and in that it is written that if we use fastq-dump --split-3 SRR786.sra, then we get 3 files as i got above. Additionally SRR786.fastq file is much smaller in size than other 2 files namely SRR7861.fastq and SRR7862.fastq.
I would be really kind if you guys explain me why 3 files were generated when i did not gave the split option and also what does this small fastq file generatations means
Regards Varun
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Varun Gupta
It's documented here
section 5.5 Basic Execution of ‘fastq-dump’ Utility
"The file, ‘SRR000001.fastq’, contains fragment read sequences where only a single biological/application read exists (or remained after filtering) for a spot. The first spot in the file will look like this"...
It's not very clear to me what the "small" file is, but I guess that what you want to use are the 2 "large" ones.
Hi Nico Thanks for your reply. I read that but could not understand why 3rd file(.fastq) is even generated when i simply used the command fastq-dump and not fastq-dump --split -3.With small file i meant that the size of SRR76.fastq was too small as compared to other 2 files.
The documentation as linked indicates that the smaller file 3 the better. IT are dumped reads: "--split-3
Legacy 3-file splitting for mate-pairs used for the 1000 Genomes fastq files. First 2 biological reads satisfying dumping conditions are placed in files _1.fastq and _2.fastq. If only 1 biological read is dumpable - it is placed in *.fastq Biological reads 3 and above are ignored."
Maybe you could try -v -v -v -v
‘-v’ or ‘--verbose’ Increases the verbosity level of the program. Use multiple times for more verbosity.
Ha ha.
Really, I don't know why you are seeing what you do. Could you try getting the sra.lite version of the file instead, just to see if it's doing the same thing?
I don't know if this helps at all, but maybe check your version of the sra toolkit and contact the help desk over there if you keep having problems.
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written
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Madelaine Gogol
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perhaps _1 & _2 are paired end and the other is a single end library.
But the size of the single end library as u say is way too small as compared to _1 and _2. Any suggestions on this .
Regards Varun