You can probably use fastq-dump
to download SRR1803613.479767.1 as follows but I haven't tried paired reads, etc with this.
fastq-dump -A SRR1803613 -N 479767 -X 479767 --fasta
perfect. This is what I want. I will go for this and see what I will get and will try it for paired end reads and tell you. I will work on both.
I got an error message due to the missing parameter for the fasta option. I give a corrected example here: C: How to retrieve an individual read with fastq-dump
What do you mean by "download selected individual reads"? How do you know which reads you want to download?
fastq-dump
allows streaming the output, so you can combine it with head
to download the first whatever number of reads you want. However, there is random access to these files, so you can't access "individual" reads, and there is no way of skipping download a certain number of reads - you can combine head
and tail
, for example, but you still have to download the reads before discarding them.
I mean downloading individual reads I know their IDs just like this for example SRR123456.4564 and don't want to download the whole SRR123456 run file which may be large and will take time. Provided I want a list of reads from many SRA runs.