Hi,

The report was obtained after running fastqc on my data. However after looking at the report statistics, the Quality is not good in the Per Base Sequence Quality and there is a difference between the mean and median at each cycle. How can the quality be improved? And why is there a difference between the mean and median in the fastqc report at each cycle?

Benjy

From:

Benjamin Osei-agyeman benjy_osei@yahoo.co.uk;

To:

Ido Tamir tamir@imp.ac.at;

Cc:

galaxy-user@lists.bx.psu.edu;

Subject:

Re: [galaxy-user] Quality report

Sent:

Wed, Nov 6, 2013 5:31:22 PM

The report was obtained after running fastqc on my data, I found out that the quality of the report is not good and that the mean and median are different at each cycle. Please how can the difference between the mean and median be improved as well as improving the overall quality

From:

Ido Tamir tamir@imp.ac.at;

To:

Benjamin Osei-agyeman benjy_osei@yahoo.co.uk;

Cc:

galaxy-user@lists.bx.psu.edu;

Subject:

Re: [galaxy-user] Quality report

Sent:

Wed, Nov 6, 2013 4:38:15 PM

Please be more specific about which quality of what gets reported. Why do you think its important to reduce the difference between mean and median?

best, ido

On Nov 6, 2013, at 4:50 PM, Benjamin Osei-agyeman benjy_osei@yahoo.co.uk wrote:

Hi, After obtaining a quality report in galaxy I found out that there is a difference between the mean and median at each cycle. How can this difference be reduced using galaxy?

Thanks in advance Benjy ___________________________________________________________ The

Galaxy User list should be used for the discussion of

Galaxy analysis and other features on the public server at usegalaxy.org.  Please keep all replies on the list by using "reply all" in your mail client.  For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

To search Galaxy

mailing lists use the unified search at:

http://galaxyproject.org/search/mailinglists/