I am glad you solved your problem and thank-you for posting the resolution,
N
On Fri, Oct 10, 2014 at 11:32 AM, Salzberg, Anna <[email protected]>
wrote:
> Nils,
>
>
>
> I see I made a mistake in my countTileDups script, in that I report the
> wrong variable in the end!! The number of dups in the same tile is in fact
> > than you reported optical duplicates.
>
>
>
> So please ignore my request for now.
>
>
>
> Thank you,
>
> Anna
>
>
>
> *From:* Salzberg, Anna
> *Sent:* Friday, October 10, 2014 10:26 AM
> *To:* 'Nils Homer'
> *Cc:* [email protected]
> *Subject:* RE: [Samtools-help] Reporting Bug - Optical Duplicates of
> Picard MarkDuplicates
>
>
>
> Dear Nils,
>
>
>
> I installed Picard 1.122, and the number of optical duplicates was reduced
> by over 25% (the estimated library size was also different in the new
> version).
>
>
>
> Unfortunately, I still think that there is a bug with the number of
> optical duplicates, as simply counting the number of duplicates that have
> the same tile results in 3 orders of magnitude less than the MarkDuplicates
> optical duplicates count.
>
>
>
>
>
> I would *greatly* appreciate if you could look into this as this is super
> important to my lab. I have provided in my previous email 2 scripts; one
> of them is a very simple script (only a few lines) that simply counts
> duplicates with the same tile.
>
>
>
> Thank you very much for your help with this issue.
>
>
>
> Anna
>
>
>
> *From:* Nils Homer [mailto:[email protected]
> <[email protected]>]
> *Sent:* Thursday, October 09, 2014 4:34 PM
> *To:* Salzberg, Anna
> *Cc:* [email protected]
> *Subject:* Re: [Samtools-help] Reporting Bug - Optical Duplicates of
> Picard MarkDuplicates
>
>
>
> I am replying to the list so others can benefit from our discussion.
>
>
>
> The latest Picard release to support updated Illumina read names is 1.120
> while your install is 1.99. You will need to update to this version or the
> latest version to get the benefit of this update.
>
>
>
> Nils
>
>
>
> On Thu, Oct 9, 2014 at 4:08 PM, Nils Homer <[email protected]>
> wrote:
>
> Could you tell us what version of Picard you are using? There was an
> issue earlier with parsing read names from newer Illumina analysis software.
>
>
>
> Nils
>
>
>
> On Thu, Oct 9, 2014 at 3:00 PM, Salzberg, Anna <[email protected]>
> wrote:
>
> Hello,
>
>
>
> I am convinced that the optical duplicates count of the Picard
> MarkDuplicates command is incorrect. When I wrote a script to detect
> optical duplicates in my dataset, I got only ~1k optical duplicates as
> opposed to MarkDuplicates ~3 million. I think the problem with
> MarkDuplicates is tile related because I then wrote a super simple script
> that simply counts how many duplicates share the same tile, and that was <
> 4k, that is, 3 orders of magnitudes less than MarkDuplicates! The overall
> number of duplicates (opticals or otherwise) matched (~7 million). I'm
> convinced my script is right, as it's so simple.
>
>
>
> Remove optical duplicates script:
>
> https://gist.github.com/annasa/eef7c30152ac296bb49b
>
>
>
> Count duplicates in same tile:
>
> https://gist.github.com/annasa/f5633eecf012153a3ff2
>
> Both scripts take as input a sam file sorted on chr and startPos. They
> also assume that when the sequence name is parsed by ":" then the tile is
> the 5th field, x the 6th and y the 7th (e.g.
> HWI-ST1318:119:H89A3ADXX:1:2209:1705:6933, where tile is '2209', x is
> '1705' and y is'6933'). Finally, they assume that the file is for a single
> lane, as I was working with such files.
>
> This is VERY important for my lab. Please advise as soon as you can.
>
> Thank you,
>
> Anna
>
>
>
>
>
>
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