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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