Re: [Samtools-devel] Problem with insertSizeMetrics version 1.118

[Nils H. <nh...@br...>]

It looks like you have 30% of your paired end reads in FR orientation while
70% is in RF orientation.  The plotting script does not handle the case
where the histogram has counts for two orientations.  This is typically not
a problem since the fraction of the second most counts (FR in your case) is
below a certain threshold (see the command line option MINIMUM_PCT).  This
threshold is 5% by default.

You have a few options if you need to get these plots working:
1. Set MINIMUM_PCT=0.4 (0.5 would be better) and you will get nice plots
for the RF orientation.
2. Filter your SAM/BAM into two files, one for FR and one for RF, and run
the tool on each file individually to get two plots.
3. Submit a pull-request on github to make this work.

Thanks for reporting your problem!

Nils


On Wed, Jul 30, 2014 at 11:13 AM, Nils Homer <nh...@br...>
wrote:

> Could you attach your metrics file?
>
> N
>
>
> On Wed, Jul 30, 2014 at 10:59 AM, Sascha Meiers <sas...@em...>
> wrote:
>
>> Dear developers,
>>
>> I get an error in the latest version of Picard’s CollectInsertSizeMetrics
>> stating:
>>
>> INFO 2014-07-30 16:33:27 ProcessExecutor [1] "Not creating insert size
>> PDF as there are duplicated header names: All_Reads”
>>
>> This looks like a bug to me since the columns in the txt file are named
>>
>> insert_size All_Reads.fr_count All_Reads.rf_count
>>
>> So right now I cannot use the latest version to get the nice histograms :)
>>
>> Thanks and best regards,
>> Sascha
>>
>> PS: Rscript —-version
>> R scripting front-end version 3.1.0 (2014-04-10)
>> just in case you need that information
>>
>>
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>