fastq-dump split-spot and skip-technical

Question

[Shicheng Guo]

Hi All,

Anyone can make a clear interpretation to the split-spot and skip-technical option in fastq-dump?

--split-spot           Split spots into individual reads. (**I guess this option split each read to two parts**)
--skip-technical    Dump only biological reads.

• What does --split-spot can be used?
• What's principle of skip-technical?
• What's difference between --split-spot and --split-files?

It is very interesting to the output for:

fastq-dump -X 5 --split-spot -Z SRR390728
fastq-dump -X 5 --split-files -Z SRR390728
fastq-dump -X 5  -Z SRR390728

Thanks.

Usage:

fastq-dump -X 5 -Z SRR390728

Prints the first five spots (-X 5) to standard out (-Z). This is a useful starting point for verifying other formatting options before dumping a whole file.

fastq-dump -I --split-files SRR390728

Produces two fastq files (--split-files) containing .1 and .2 read suffices (-I) for paired-end data.

fastq-dump --split-files --fasta 60 SRR390728

Produces two (--split-files) fasta files (--fasta) with 60 bases per line ("60" included after --fasta).

fastq-dump --split-files --aligned -Q 64 SRR390728

Produces two fastq files (--split-files) that contain only aligned reads (--aligned; Note: only for files submitted as aligned data), with a quality offset of 64 (-Q 64) Please see the documentation on vdb-dump if you wish to produce fasta/qual data.

Done

[GenoMax]

Are you bumping your own/old threads up to the main page for some specific reason?

Answer 1

[rrr]

Each "spot" is like a piece of DNA, so a spot groups together all the technical reads and forward and reverse reads if the data is paired end.

You probably want to skip-technical because that tells it to not bother downloading the barcodes and primers (all the data will be de-multiplexed into separate SRR's corresponding to sample names in the (hopefully provided) metadata anyway).

You DEFINITELY want to split somehow, otherwise it just pastes the forward and reverse together in one long line which is unbelievably stupid and also ironically an un-allowed upload format. split-spot will give you an 8-line fastq format where forward precedes reverse. split-files will give you two fastq files, one with forward and one with reverse. (If you do split-files and not skip-technicals you'll also get another fastq file for the primer/barcode reads) I use the split-files format because it easily feeds into mothur's make.files and make.contigs commands.

This blog post is super helpful and goes into more detail.

Answer 2

[Larissa Graciano]

The link to the blog post isn't working, I believe this is the updated one: https://edwards.flinders.edu.au/fastq-dump/