faste-dump for single-end data

Question

[eva.lucarelli]

Hello everyone!

I am currently trying to convert a .sra file to a .fastqc file using the fastq-dump tool.

Here is the line of code we've learnt in class to do so:

fastq-dump --split-files --gzip --skip-technical --readids --read-filter pass --clip SRR12737830

I was wondering if the "--split-files" was very useful given the fact that my reads are not paired-end... Can anyone help me out on this?

Thanks in advance for your answer!

Eva

Answer 1

[GenoMax]

If this is single end data then there is no need to use --split-files.

[eva.lucarelli]

Thank you so much for your fast answer!

And what about the —clip? I found that it adds left and right clips, but this explanation doesn’t really help me... Forgot to mention that the line of code I’ve learnt was applied to paired-end data.

[GenoMax]

I would suggest that you just dump the reads out. This looks like a smallRNA seq experiment. You should manage adapter clipping based on kit/method used.

[eva.lucarelli]

So the —clip option just gets us rid of the adapters on each side of the reads? Are there adapters on both ends in single-end sequencing, or just on one? Thank you so much for answering all these questions, I am very very new to fastq-dump and I must admit that I am a bit lost!

[GenoMax]

In Illumina sequencing adapter sequence should appear only on the 3'-end of a read in single or paired-end sequencing (unless some custom scheme is being used). Small RNA sequencing may use special adapters that are specific for kits/method used to make the libraries and thus may need special handling. In case of small RNA the actual part of interest from a 50 bp read may only be the first ~25 bp.