I have being trying to get fastq files from sra data of SRR1030614. This is registered as paired-end, so I tried as follows.
$ fastq-dump --split-files SRR1030614
As the result, I got SRR1030614_2.fastq, but not SRR1030614_1.fastq. In addition, I got the following message from fastq-dump program:
Rejected 27168787 READS because READLEN < 1 Read 27168787 spots for SRR1030614.sra Written 27168787 spots for SRR1030614.sra
When I checked the entry SRR1030614 on NCBI SRA, in the "Reads" tab I see the read data such as
Reads (separated) >gnl|SRA|SRR1030614.1.1 1 (Technical) Empty read >gnl|SRA|SRR1030614.1.2 1 (Biological) CTGATCCGAACATTGTGTACATGACCATTTCGATGATGTACAGTACAATCGTCACATAGA AGATAACCCGCCACGCGCTAATTGTTTGGTTGCCGTGTGTG
So maybe I cannot get the SRR1030614_1.fastq file because it is empty? Also, if I cannot have two separate fastq files, is it ok to run the downstream analysis (e.g. trinity) specifying the read file is single-ended? Any comments will be much appreciated. Thank you.