I am using SRA Toolkit for SRA Reads from NCBI web page. I went through the mannual and came up of using this command: ~/bin/sratoolkit.2.7.0-centos_linux64/bin/fastq-dump --split-files --fasta 60 SRR1981235 I thought I will download the SRA files and will split into two files. It created two fasta files as fasta.1 and fasta.2 (paired reads). But for aligment it says the number of reads are not equal. I am very new for this and I need advise. Regards!
Ive just checked your command and downloaded the 2 fastq files and followed it with the line count (wc -l) with these results:
So the lines are all paired - I think youve had an interuppted download....try it again. both files downloaded should be 2.4G each.
Then do wc -l to make sure you get the same result as me. All should be good then.
I have question. When I used --split-3 rather than -split-files, I got three output. When I looked for manual of fastqdump it says that the reads satisfying biological condition are put as _1.fasta and _2.fasta. And if only one read present it is given as fasta. Here I do not understand for what fastq is considering as biological condition. Can anyone helo me for this please?