Raw Illumina Data

Question

[Cdiez]

Hello,

I have just received the raw data of an Illumina genomic library (one line) so I already have a 6GB fastq file. I know I have to trim the adaptors and condense de files taking only the "unique" sequences. But, is there any package able to do this process? I mean, processing the "raw" data of a library, or os writing your own perl scripts the only way to face the problem?

Thanks in advance!

Answer 1

[Swbarnes2]

Most genomic libraries don't have problems with adaptors. They only crop up when the sequences that one wants sequenced are very short. You probably have 60-100 bases of a 200+ base DNA insert, so you won't see adaptors.

Usually, duplicates are figured out after alignment, not before. Computationally, it's easier on a sorted .bam than on raw reads, if you go by coordinates.

[Cdiez]

Thanks! yes I have this problem with the adaptors because I am sequencing small RNA (20-30 nt) then I have to trim them before starting the analysis.

[Jeremy Leipzig]

there are a few adapter trimming solutions out there: http://seqanswers.com/forums/showthread.php?t=1159

[Cdiez]

Thanks! I appreciate your help! I'm also checking fastx toolkit and it seems quite useful.

Answer 2

[Ido Tamir]

The fastx toolkit provides some simple to use command line utilities to do this.

Answer 3

[Darked89]

Check Tagdust from: http://genome.gsc.riken.jp/osc/english/dataresource/

If you need to do the oposite (select fastq reads with certain pattern) there is fqgrep: https://github.com/indraniel/fqgrep

Answer 4

[Bach]

Filtering for unique sequence is a very bad habit I never understood why people would even envisage doing that: you enrich for sequencing errors.

[Ying W]

see http://seqanswers.com/forums/showthread.php?t=6854

Answer 5

[Ying W]

You can use FastQC to figure out if you have adapter issues and also base bias.