Question: Insertion size metrics
gravatar for hsuehyuanc
4.6 years ago by
United States
hsuehyuanc0 wrote:


I met a problem when I try to determine the insert size of my paired end RNA-seq data.

Usually the output looks like:

155 433

156 522

157 488

158 516

However, my output is:

29 0 0 1

30 1 0 1

31 0 0 1

32 0 0 1

33 1 0 0

Why the output has so may numbers after the insert size and why the numbers are all so low


Thank you,



galaxy • 980 views
ADD COMMENTlink modified 4.6 years ago by Jennifer Hillman Jackson25k • written 4.6 years ago by hsuehyuanc0
gravatar for Jennifer Hillman Jackson
4.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This just looks like a more detailed output option for this tool. Click on the blue double arrow "rerun" button for the job's dataset to bring back up the tool form with the original settings. Now examine the last option on the form named "Metric Accumulation Level". A selection other than "All reads (default)" produces this type of output.

Now go back and look at this output. In the header line immediately above the statistics, you will see the labels for the values associated with the form selection made. These will be a breakdown that looks something like:

insert_size ​All_Reads.fr_count <some_label>.fr_count <some_label>.fr_count

You can certainly re-run with the default, or use this if it is wanted now that it is explained,

Best, Jen, Galaxy team

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Jennifer Hillman Jackson25k
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