QA with ShortRead

[dawe]

Hi all,
Is anybody here using ShortRead package (in R) to produce QC reports? And if so, is there anybody who produce QC reports without using Eland to align reads?
Of course, if you have any suggestion for an alternative QC package, suggest!

d

[KevinLam]

I am aware of DNAA http://seqanswers.com/wiki/DNAA but it probably requires BFAST alignment so maybe that doesn't help?

[simonandrews]

Hi all,
Of course, if you have any suggestion for an alternative QC package, suggest!

Not using R, but we produce FastQC which does QC reports on unmapped sequence files. The other popular package for this is the FastX toolkit

[maplesword]

Not using R, but we produce FastQC which does QC reports on unmapped sequence files. The other popular package for this is the FastX toolkit

I use FastQC, and I think it is really an amazing tool

[nilshomer]

I am aware of DNAA http://seqanswers.com/wiki/DNAA but it probably requires BFAST alignment so maybe that doesn't help?

It doesn't require BFAST alignments, just the install requires the BFAST code since to use the reference API.

[bio_jit]

qcqr is one very good bioconductor package I am using! try it ! may be it work for you