Hi Terry,
Katie Hyma kindly tested the TagCountToFastqPlugin that Jeff wrote against the
MergeMultipleTagCountPlugin. In brief, the TagCountToFastqPlugin produces one
more sequence in the fastq file than the MergeMultipleTagCountPlugin for the
same operation. This is likely some kind of fence post error.
In the case of the build, this means potentially loosing 1 tag out of 97M, not
a huge loss. But we should see if we can find and fix the bug. See below for
more details.
Best,
Rob
On Thursday, August 30, 2012 12:59:46 PM Katie Hyma wrote:
> Hi Rob,
>
> I finally ran the reference pipeline again, so I tested this plugin. I
> used a .cnt file produced with the -MergeMultipleTagCountPlugin in
> Tassel Version: 3.0.128 as input, then ran the new plugin in the most
> current version of Tassel 3 (Tassel Version: 3.0.129 Date: August 30,
> 2012) and the most current version of Tassel 4( Tassel Version: 4.1.2
> Date: August 30, 2012) to generate .fq files, and compared each output
> to the .fq file that was generated with Tassel 3.0.128
>
> The parameters used with the old version of the plugin:
>
> -fork1 -MergeMultipleTagCountPlugin -i tagcountdir -o
> safflower_reference.fastq -c 5 -t -endPlugin -runfork1
>
>
> The parameters used to test the new plugin (same command with both
> Tassel 3 and Tassel 4)
>
> -fork1 -TagCountToFastqPlugin -i safflower_reference.cnt -o
> safflower_reference.fastq.fq.testT3 -c 5 -endPlugin -runfork1
>
> The output of the new plugin was the same for Tassel 3 and Tassel 4.
> When comparing to the .fq file produced with the old plugin, there is
> one tag that shows up in the .fq file from the new plugin that did not
> show up in the old .fq file. It is the last tag output to the new .fq
> file(s).
>
> diff output:
>
> 7674860a7674861,7674864
>
> > @length=64count=5
> > TGCATTTTTTTTTTTTTTTTGGTTTTGGTTCATCGGCCTAACAGCCCCTCAAAAAATTTATGCA
> > +
> > ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
>
> I have no idea why it would be so, maybe there was an off by one
> counting error in a loop somewhere?
>
> When I use the old plugin with the new version of tassel, I get the
> same result as the old plugin with the old version of tassel (ie the
> old plugin is consistent between builds).
>
> Let me know if you need any more info or want the files.
>
> Best,
> Katie
