Hi, I have downloaded sra file from NCBI, SRR4242282.sra and I got three fastq files after use fastq-dump to extract fastq files from sra files. command :fastq-dump --split-3 --gzip SRR4242282.sra I have no idea with this result, I haven't met this before. Any suggestion would be appreciated.
Please see my previous post: this is due to the fact that BOTH paired and unpaired reads are included in these sra files. Using the
--split-files option does not work since this would lead to fastq-files that are incomplete. What you did is correct; simply use the files ending with
_2 will do. The remaining files contains the unpaired reads, and can be trashed.
Either use only the _1 and _2 files or use option
--split-files instead of
See the manual/help page:
--split-files Dump each read into separate file.Files will receive suffix corresponding to read number --split-3 Legacy 3-file splitting for mate-pairs: First biological reads satisfying dumping conditions are placed in files *_1.fastq and *_2.fastq If only one biological read is present it is placed in *.fastq Biological reads and above are ignored.