Do quality control on outliers

[qtran1]

Perform FastQC on the sequence reads of the two samples that appear to be outliers, according to the PCA graph.

[davebridges]

Actually, can you run FastQC on all of them. It might be easier to run it
on a script (I think fastqc can be run from the command line). If there is
one sample/lane combo that is bad its probably worth knowing.

On Sat, Jun 21, 2014 at 9:38 AM, Quynh Tran notifications@github.com
wrote:

Perform FastQC on the sequence reads of the two samples that appear to be
outliers, according to the PCA graph.

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[qtran1]

True, I was thinking of running all anyway. I think this step should be a default step in our pipeline from now on.

[davebridges]

i totally agree

On Sat, Jun 21, 2014 at 9:54 AM, Quynh Tran notifications@github.com
wrote:

True, I was thinking of running all anyway. I think this step should be a
default step in our pipeline from now on.

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[qtran1]

Install and try RSeQC after hera up and running.

[davebridges]

This looks like it does a lot of post-mapping analysis rather than read
quality checks. Does it check quality scores and bias effects like fastqc
does, or are you planning to do both?

On Sun, Jun 22, 2014 at 12:05 PM, Quynh Tran notifications@github.com
wrote:

Install and try RSeQC after hera up and running.

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[qtran1]

I want to do both.

On Jun 22, 2014, at 12:28 PM, Dave Bridges wrote:

This looks like it does a lot of post-mapping analysis rather than read
quality checks. Does it check quality scores and bias effects like fastqc
does, or are you planning to do both?

On Sun, Jun 22, 2014 at 12:05 PM, Quynh Tran <notifications@github.commailto:notifications@github.com>
wrote:

Install and try RSeQC after hera up and running.

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Reply to this email directly or view it on GitHubhttps://github.com//issues/1#issuecomment-46787113.

[qtran1]

RSeQC has quality control too such as base calling quality, GC content, nucleotide composition bias. I'll do both FastQC and RSeQC this time, but I think in the future RSeQC may be enough