programs for filtering low complexity

swarbre · 11-07-2009, 01:02 PM

This question was asked elsewhere but I have the same question as below, any help.

1) I have many "low-complexity" reads. Some are simply polyA, polyC,
> etc. But some others are runs of "ATATAT" or "CACACACA", etc. Previously
>
> I would have used "dust" on the command line to filter out this kind of
> read in a fasta file. Any ideas on how to achieve similar functionality
> in the ShortRead world?

olus · 12-14-2009, 07:19 AM

Look at :

https://stat.ethz.ch/pipermail/bioc-...ch/000191.html

http://www.mail-archive.com/bioc-sig.../msg00148.html

Though not a ShortRead package:
http://genome.gsc.riken.jp/osc/engli...rc/tagdust.tgz

Cheers

mdaskal · 02-04-2012, 10:46 PM

Hi,

I am looking for a definition of low complexity reads for reads of variable lengths (about 100 nucleotides long).

Right now, I am using the following definition:
- Divide a read in subsegments of 32 nucleotides. (last subsegment is overlapping one before last)
- Count number of unique tri-nucleotides in each segment.
- If number of unique tri-nucleotides is smaller than 5, then the segment is of "low complexity"
- If there is at least one "low complexity" segment, the read is considered "low complexity"

Comments regarding the relevancy of this definition would be appreciated.

Regards, Michael.

dan · 02-05-2012, 06:05 AM

Quote:

Originally Posted by mdaskal

Hi,

I am looking for a definition of low complexity reads for reads of variable lengths (about 100 nucleotides long).

Right now, I am using the following definition:
- Divide a read in subsegments of 32 nucleotides. (last subsegment is overlapping one before last)
- Count number of unique tri-nucleotides in each segment.
- If number of unique tri-nucleotides is smaller than 5, then the segment is of "low complexity"
- If there is at least one "low complexity" segment, the read is considered "low complexity"

Comments regarding the relevancy of this definition would be appreciated.

Regards, Michael.

Why 5?

How does your operational definition compare to SEG / Dust?

mdaskal · 02-05-2012, 06:46 AM

Hi Dan,

I am not familiar with the definition of SEG / Dust.
Where can I find some details about it?

Would you suggest another limit than 5 unique tri-nucleotides (higher?lower?)?

Regards, Michael.

dan · 02-05-2012, 08:04 AM

I guess they are both in PubMed? Internet is slow here atm or else I'd link...

I don't suggest an alternative without data... so my question really was, did you analyse / benchmark your metric? i.e. what fraction of reads are low complexity at 3, 4, 5, 6, etc...

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11-07-2009, 01:02 PM	#1
swarbre Member Location: CA Join Date: Sep 2009 Posts: 11	programs for filtering low complexity This question was asked elsewhere but I have the same question as below, any help. 1) I have many "low-complexity" reads. Some are simply polyA, polyC, > etc. But some others are runs of "ATATAT" or "CACACACA", etc. Previously > > I would have used "dust" on the command line to filter out this kind of > read in a fasta file. Any ideas on how to achieve similar functionality > in the ShortRead world?

02-05-2012, 06:46 AM	#5
mdaskal Junior Member Location: Israel Join Date: Feb 2012 Posts: 2	Low complexity reads Hi Dan, I am not familiar with the definition of SEG / Dust. Where can I find some details about it? Would you suggest another limit than 5 unique tri-nucleotides (higher?lower?)? Regards, Michael. Last edited by mdaskal; 02-05-2012 at 07:07 AM.

02-05-2012, 08:04 AM	#6
dan wiki wiki Location: Cambridge, England Join Date: Jul 2008 Posts: 266	I guess they are both in PubMed? Internet is slow here atm or else I'd link... I don't suggest an alternative without data... so my question really was, did you analyse / benchmark your metric? i.e. what fraction of reads are low complexity at 3, 4, 5, 6, etc... __________________ Homepage: Dan Bolser MetaBase the database of biological databases.

12-14-2009, 07:19 AM	#2
olus Member Location: milan, italy Join Date: Aug 2008 Posts: 22	Look at : https://stat.ethz.ch/pipermail/bioc-...ch/000191.html http://www.mail-archive.com/bioc-sig.../msg00148.html Though not a ShortRead package: http://genome.gsc.riken.jp/osc/engli...rc/tagdust.tgz Cheers

02-04-2012, 10:46 PM	#3
mdaskal Junior Member Location: Israel Join Date: Feb 2012 Posts: 2	Hi, I am looking for a definition of low complexity reads for reads of variable lengths (about 100 nucleotides long). Right now, I am using the following definition: - Divide a read in subsegments of 32 nucleotides. (last subsegment is overlapping one before last) - Count number of unique tri-nucleotides in each segment. - If number of unique tri-nucleotides is smaller than 5, then the segment is of "low complexity" - If there is at least one "low complexity" segment, the read is considered "low complexity" Comments regarding the relevancy of this definition would be appreciated. Regards, Michael.