Question: Error Running The Picard Tool?

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Dottorini, Tania •

**20**wrote:Hi,
I am trying to determine the mean inner distance between mate pairs,
but encountered odd results. Briefly, to calculate the mean inner
distance I mapped PE data with 2x100bp read length with Bowtie against
the reference transcriptome, and used the Picard InsertSize Metrics to
calculate the Mean insert size. I then, subtracted the combined insert
size (2*100) from the Mean insert size value, thus obtaining the mean
inner distance between mate pairs. In all the cases studied, 4 samples
and 4 controls, I have always obtained negative mean inner distance
between mate pairs values. In addition, in some cases I had the
following error running the Picard Tool:
"Unable to find expected pdf file
/galaxy/main/jobdir/006/471/.
../InsertSizeHist.pdf
This always happens if single ended data was provided to this tool"
But in all cases I can confirm I provided paired-end NGS data. For
same of the runs that gave me this failure log, I rerun them again but
mapping to the genome instead of the transcriptome, and in this case
it did work but always giving me negative distance values.
I would like to know if this is the correct procedure to be followed
or if there are other approaches I can use to find these distance
values and if I can eventually use such negative distance values in
Tophat
Thank you for your help
Tania

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modified 4.8 years ago
by
Jennifer Hillman Jackson ♦

**25k**• written 4.8 years ago by Dottorini, Tania •**20**