454 Data cleaning - Page 2

Jose Blanca · 06-12-2011, 11:50 PM

I think that I have fixed the problem. The fix is included in the psubprocess that I have just released, could you try to reinstall psubprcess with this version?

grassgirl · 06-14-2011, 12:56 PM

Quote:

Originally Posted by Himalaya

Hi Jose
I am trying to do quality trimming and filtering 454 reads. The adaptors and primers and barcode sequences are already removed.I am not allowed to specific minimum quality threshold to clean bad quality reads. I don't understand why? How does it do quality trimming.
thnx

I am wondering this myself. We have a Junior with v.2.5p1 software and it appears (by scanning many qual scores) that the lower cutoff is 10, although I see a few zeros in there (is this a glitch)? I looked through the GS Run section of the manual on filtering and could not find a place to set the qual score threshold nor an explanation of what the cutoff is. I'd hate to assume it is 10 based on a visual scan of some qual scores. Anybody have an idea?

Jose Blanca · 06-14-2011, 11:51 PM

I would recommend to to a quality boxplot to understand how every run went. You have an example of a boxplot here:

http://bioinf.comav.upv.es/courses/s...ead-statistics

It is the thrid chart.

grassgirl · 06-15-2011, 10:35 AM

Thank you, Jose. After looking at the link you sent, I found that our bioinformatics center has a program to do just that. I am completely new to sequencing so I appreciate your help.

Himalaya · 06-26-2011, 02:30 AM

Quote:

Originally Posted by essvee

I suggest trying SeqTrim.
You can set minimum quality based on a defined window size, minimum length, etc.
You can also run it command line, or online.
www.scbi.uma.es/seqtrim/

hi essvee
Do you know how seqtrim cleans up the low quality bases. I mean the actual steps or methodology? My sequences are already clean from primers and adaptors. I just need to clean low quality bases. I couldn't find it in published papers(2007 and 2010) and in downloaded tar file. Please let me know where i can find the working principle of cleaning low quality bases.
Thanks

Himalaya · 06-27-2011, 06:08 AM

Quote:

Originally Posted by robs

I like PRINSEQ (http://prinseq.sourceforge.net/). It comes as web and standalone version and does all the QC and data pre-processing that you need.

The application note also contains a short comparison with similar tools (http://bioinformatics.oxfordjournals.../27/6/863.long).

HI Rob
Can you show me where can i find the working principle of prinseq? I would like to know how prinseq trims off the low quality score bases?

Himalaya · 08-22-2012, 05:53 AM

Finally I got QTrim to quality trim the 454 sequence reads. It also outputs the graphical plots showing the quality trend of reads before and after quality trimming. QTrim is available here
hiv.sanbi.ac.za/software/qtrim

maryluzyl · 10-23-2013, 01:42 PM

Hi
someone knows how to change parameters in seqTrim by command line
Thanks so much
Mary Luz

JackieBadger · 10-23-2013, 02:33 PM

any 454 data should always be re-called using PyroBayes....much more accurate base-caller and significantly improves data quality

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06-12-2011, 11:50 PM	#21
Jose Blanca Member Location: Valencia, Spain Join Date: Aug 2009 Posts: 70	I think that I have fixed the problem. The fix is included in the psubprocess that I have just released, could you try to reinstall psubprcess with this version?

06-14-2011, 11:51 PM	#23
Jose Blanca Member Location: Valencia, Spain Join Date: Aug 2009 Posts: 70	I would recommend to to a quality boxplot to understand how every run went. You have an example of a boxplot here: http://bioinf.comav.upv.es/courses/s...ead-statistics It is the thrid chart.

06-15-2011, 10:35 AM	#24
grassgirl Member Location: Oregon, USA Join Date: Mar 2011 Posts: 51	Thank you, Jose. After looking at the link you sent, I found that our bioinformatics center has a program to do just that. I am completely new to sequencing so I appreciate your help.

08-22-2012, 05:53 AM	#27
Himalaya Member Location: uk Join Date: Jun 2010 Posts: 38	Finally I got QTrim to quality trim the 454 sequence reads. It also outputs the graphical plots showing the quality trend of reads before and after quality trimming. QTrim is available here hiv.sanbi.ac.za/software/qtrim

10-23-2013, 01:42 PM	#28
maryluzyl Junior Member Location: Bogota, Colombia Join Date: Apr 2013 Posts: 2	Hi someone knows how to change parameters in seqTrim by command line Thanks so much Mary Luz

10-23-2013, 02:33 PM	#29
JackieBadger Senior Member Location: Halifax, Nova Scotia Join Date: Mar 2009 Posts: 381	any 454 data should always be re-called using PyroBayes....much more accurate base-caller and significantly improves data quality