Life cycle of a fastq file

Question

[edrezen]

Hello,

I am curious about the life cycle of NGS sequencing files (like fastq files) once they have been generated. I suppose the answer strongly depends on the biological field but are there some general trends ?

My questions are :

• what is the first tool you use for processing a brand new fastq file ?
• when your data analysis is finished, what is the last processing you do on it ? store it somewhere forever ? get rid of it ?

Thank you.

Answer 1

[Devon Ryan]

The first thing I use is either FastQC or a trimmer, generally a trimmer (I typically run FastQC on the trimmed file). I'm increasingly becoming a fan of simply deleting fastq files after mapping. BamHash (I have a fork with an extra tool that I find useful) is really handy in this regard, since it allows ensuring that fastq files can be reconstructed from the alignment files.

[edrezen]

Oh thanks, I didn't know BamHash.

[Devon Ryan]

I wouldn't have either were it not for twitter :)

Answer 2

[reza.jabal]

This paper thoroughly answers your questions:

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4179624/

[edrezen]

Thanks for the link, it seems interesting.

Note that I am also curious about other fields than exome sequencing. For instance, people who work in metagenomics may have also interesting insights.

Answer 3

[Nicolas Rosewick]

it depends really on the library type (RNA-Seq, Chip-Seq, DNA-Seq, .... ). But you could use a quality control tool as fastqc to check your fastq.

Answer 4

[Madelaine Gogol]

+1 for fastqc.

As far as the life cycle goes, our institute has a systematically organized file system holding many of the old gzipped fastq files. Occasionally, people want to revisit the old data, and it's one way to ensure you're really starting from the raw data. I'm not sure how long this will continue, but it's what we're doing for now.