flash histogram output

[ronaldrcutler]

Hello all. in the output after running flash there is a histogram labeled out.histogram which gives a plot and out.hist which gives values that can be used to make a histogram, I believe.

My question is, what does this histogram represent?

Thanks

[Markiyan]

Flash histogram represents combined reads template size distribution.

Dear FLASH user,

The flash *.histogram represents the distribution of the library template sizes for combined reads, with 1bp step.
[Template Length] [#*'s proportional to template count]

225 *****
226 ********
227 ******

there are also *.hist file(s)
[Template Length][TAB][Template Count]
225 5000
226 8000
227 6000

[ronaldrcutler]

Thanks for the clarification. What are you specifically referring to by library template sizes for combined reads? Does this mean how many reads were identified with this size?

[Markiyan]

Thanks for the clarification. What are you specifically referring to by library template sizes for combined reads?

Yes I was.

Does this mean how many reads were identified with this size?

Yes it does.

PS: If the read quality clipping is not stringent enoughf (epc>2) - more than 2 errors per 10bp - than it would not combine those reads (unless you turn on the "--allow-outies" option, than it may combine those reads if the template is shorter, than the read length).