download with fastq-dump

NDUFB11 · 02-13-2019, 12:24 PM

Hello everyone, I'm still new to RNAseq and I hope I can find someone to help me out with my question.

I want to download RNAseq data (SRR) using SRA Toolkit which I already installed have on my macbook.

this is the link from where I want to download the data
https://www.ncbi.nlm.nih.gov/sra/?term=SRR359063

I created a folder named processing and a subfolder named raw to where I want to put this data files.
The command line is this one

Patrizios-MBP:raw patrizio$ fastq-dump --outdir raw/ --split-3 --gzip SRR359063

why do I get this?

-bash: fastq-dump: command not found

what is missing?

thank you

GenoMax · 02-13-2019, 12:45 PM

The directory you have the program "fastq-dump" is likely not in your $PATH ( a set of directories that are automatically searched when you try to run something). You could try ./fastq-dump if the executable is in the directory where you are running this from.

I suggest you save yourself the hassle and download fastq files directly from EBI-ENA here.

You may want to learn unix basics by using this tutorial, if you are not familiar with command line.

NDUFB11 · 02-13-2019, 01:12 PM

The suggestion turned out very useful and I'm downloading the files.
I'm doing a course this days I wanted to practice and understand better by repeating what we did on my machine so it might be that the executable is not in my path?
hope the informations below can tell that

Patrizios-MBP:sratoolkit.2.9.4-mac64 patrizio$ ls
CHANGES README-blastn README-vdb-config README.md bin example schema
Patrizios-MBP:sratoolkit.2.9.4-mac64 patrizio$ ./fastq-dump
-bash: ./fastq-dump: No such file or directory

thank you

GenoMax · 02-13-2019, 04:29 PM

Correct. That executable is likely in the "bin" directory that you see above. So you could have run it by saying

Code:

$ bin/fastq-dump --outdir raw/ --split-3 --gzip SRR359063

NDUFB11 · 02-13-2019, 10:13 PM

It worked

thank you!!

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02-13-2019, 12:24 PM	#1
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	download with fastq-dump Hello everyone, I'm still new to RNAseq and I hope I can find someone to help me out with my question. I want to download RNAseq data (SRR) using SRA Toolkit which I already installed have on my macbook. this is the link from where I want to download the data https://www.ncbi.nlm.nih.gov/sra/?term=SRR359063 I created a folder named processing and a subfolder named raw to where I want to put this data files. The command line is this one Patrizios-MBP:raw patrizio$ fastq-dump --outdir raw/ --split-3 --gzip SRR359063 why do I get this? -bash: fastq-dump: command not found what is missing? thank you

02-13-2019, 04:29 PM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	Correct. That executable is likely in the "bin" directory that you see above. So you could have run it by saying Code: $ bin/fastq-dump --outdir raw/ --split-3 --gzip SRR359063

02-13-2019, 12:45 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,087	The directory you have the program "fastq-dump" is likely not in your $PATH ( a set of directories that are automatically searched when you try to run something). You could try ./fastq-dump if the executable is in the directory where you are running this from. I suggest you save yourself the hassle and download fastq files directly from EBI-ENA here. You may want to learn unix basics by using this tutorial, if you are not familiar with command line.

02-13-2019, 01:12 PM	#3
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	The suggestion turned out very useful and I'm downloading the files. I'm doing a course this days I wanted to practice and understand better by repeating what we did on my machine so it might be that the executable is not in my path? hope the informations below can tell that Patrizios-MBP:sratoolkit.2.9.4-mac64 patrizio$ ls CHANGES README-blastn README-vdb-config README.md bin example schema Patrizios-MBP:sratoolkit.2.9.4-mac64 patrizio$ ./fastq-dump -bash: ./fastq-dump: No such file or directory thank you

02-13-2019, 10:13 PM	#5
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	It worked thank you!!