I'm trying to merge F and R files from Illumina sequencing in order to use them in the redkmer pipeline ( github.com/genome-traffic/redkmer-hpc).

I tried many options including:

-Download the reads from the SRA archive in the merged format (failed)

-Merge the reads using pandaseq (done)

-Use fastq-dump --split function (impossible to install SRA toolkit correctly)

Since I'm having some problem with the reads merged using pandaseq i want to try to use other strategies.

Do you have any suggestions?

Also, do you know how to download SRA-toolkit in the correct way?
Is it possible to use just sudo command in ubuntu instead of downloading the zipped folder?



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