Question: bamCount paired.end arg
1
4.0 years ago by
Germany
katarzyna.wreczycka10 wrote:

Hi,

How is it with the bamCount function - does it still have option paired.end="extend"? What does it mean when paired.end="filter" (it is not written in the documentation of the function)?

> bamsignals_bamCount=bamsignals::bamCount(signal1, windows, verbose=FALSE, paired.end="extend")
Błąd w poleceniu 'match.arg(paired.end)':
'arg' should be one of “ignore”, “filter”, “midpoint”

Thanks,  Kasia

bamsignals • 485 views
modified 4.0 years ago by mammana20 • written 4.0 years ago by katarzyna.wreczycka10
1
4.0 years ago by
mammana20
European Union
mammana20 wrote:

Hi Kasia,

That's correct, the bamCount function does not have the option paired.end="extend". It wouldn't make sense, because bamCount counts the 5' end of a read, so if you extend it to the whole fragment the 5' end actually does not change.

This is what the docs say about the "filter" option:

If ‘paired.end!="ignore"’ then only first reads in proper mapped pairs will be consider (i.e. in the flag of the  read, the bits in the mask 66 must be all ones)

so when you set paired.end="filter", only one read per pair will be counted (the first in the pair).

Let me know if I can help!

Alessandro