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[Khan, Anar]

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Subject: khmer Digest, Vol 11, Issue 7

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Today's Topics:

   1. Questions about abundance-dist-single.py (Tamer Mansour)
   2. Re: Questions about abundance-dist-single.py (C. Titus Brown)
   3. Re: Questions about abundance-dist-single.py (Qingpeng Zhang)


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Message: 1
Date: Sun, 22 Dec 2013 23:28:49 -0500
From: Tamer Mansour <drtamermansour at gmail.com>
Subject: [khmer] Questions about abundance-dist-single.py
To: khmer at lists.idyll.org
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        <CAG_=aot-aAyRjAGUcg=GM+KGSPdJT8seORFYZSrHRWWfdg4Fsw at mail.gmail.com>
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Hi,
I have couple questions about the "abundance-dist-single.py"
1) The input file: should I concatenate the single reads files to the interleaved paired-ended files?
2) Does the '-b' option increase or decrease the chance of false positive results? is not recommended to be used?
3) Does the '-savehash' option requires increasing the job resources (either time or ram)?

Thank you

Tamer
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Message: 2
Date: Sun, 22 Dec 2013 21:13:29 -0800
From: "C. Titus Brown" <ctb at msu.edu>
Subject: Re: [khmer] Questions about abundance-dist-single.py
To: Tamer Mansour <drtamermansour at gmail.com>
Cc: khmer at lists.idyll.org
Message-ID: <20131223051329.GA16021 at idyll.org>
Content-Type: text/plain; charset=us-ascii

On Sun, Dec 22, 2013 at 11:28:49PM -0500, Tamer Mansour wrote:
> I have couple questions about the "abundance-dist-single.py"
> 1) The input file: should I concatenate the single reads files to the
> interleaved paired-ended files?

Doesn't matter, but you will need everything you want to count in a single file.

> 2) Does the '-b' option increase or decrease the chance of false
> positive results? is not recommended to be used?

-b makes the maximum count be 255.  Probably not a good idea for mRNAseq, but probably fine for genome counting.

> 3) Does the '-savehash' option requires increasing the job resources
> (either time or ram)?

Only the time it takes to save the file to disk.

cheers,
--t
--
C. Titus Brown, ctb at msu.edu



------------------------------

Message: 3
Date: Mon, 23 Dec 2013 00:18:33 -0500
From: Qingpeng Zhang <qingpeng at gmail.com>
Subject: Re: [khmer] Questions about abundance-dist-single.py
To: Tamer Mansour <drtamermansour at gmail.com>
Cc: khmer at lists.idyll.org
Message-ID:
        <CAFeT5M6dzh-cnG6YYSVvvg4g3U+F0X9WX6vc-ZGo5ce+tikv7w at mail.gmail.com>
Content-Type: text/plain; charset=windows-1252

I also have some explanations below, maybe supplementary to Titus' answer.

On Sun, Dec 22, 2013 at 11:28 PM, Tamer Mansour
<drtamermansour at gmail.com> wrote:
> Hi,
> I have couple questions about the "abundance-dist-single.py"
> 1) The input file: should I concatenate the single reads files to the
> interleaved paired-ended files?

abundance-dist-single.py  is a single-step/in-memory version of
abundance-dist.py; no counting hash file will be created unless
?savehash is specified. It is good for counting k-mer in single(one)
sequence file.
This has nothing to do with the concept of  single-ended/paired-ended files.
 If you want to count k-mers in multiple files, use
load-into-counting.py and abundance-dist.py.


> 2) Does the '-b' option increase or decrease the chance of false positive
> results? is not recommended to be used?

If  ?-b? option is turned on, this script is constant memory, k-mer
counts will stop at 255.
This should not influence the false positive rate of counting. Only
the counting frequency of high abundance k-mers will not be at most
255 even though the real frequency is higher. If you can tolerate the
counting inaccuracy of those high abundance k-mers. You can turn it on
for it will save memory usage.

> 3) Does the '-savehash' option requires increasing the job resources (either
> time or ram)?

It will only save the hash on the hard disk for further use. So it
will not increase time or memory usage.
But it will consume some hard disk storage.

There some more explanations of the scripts here:
http://khmer.readthedocs.org/en/latest/scripts.html



>
> Thank you
>
> Tamer
>
> _______________________________________________
> khmer mailing list
> khmer at lists.idyll.org
> http://lists.idyll.org/listinfo/khmer
>



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