Question: Mean insert size and Mean inner distance between mate pairs
0
gravatar for manekineko
2.4 years ago by
manekineko90
Bulgaria
manekineko90 wrote:

Hi,

I'm confused are these two the same or different values?
I have tun Picard for calculate Mean Insert size of subset of my RNA-seq FASTQ mapped to cDNA (100bp reads) and it gives me:

MEDIAN_INSERT_SIZE         176
MEDIAN_ABSOLUTE_DEVIATION  39
MIN_INSERT_SIZE            12
MAX_INSERT_SIZE            6467
MEAN_INSERT_SIZE           193.140364

So what value should I feed to Tophat - Mean inner distance between mate pairs? 193 or?
And then somewhere I saw which confused me more ---> Mean inner distance between mate pairs = mean insert-size-2*read_length

 

 

rna-seq • 2.5k views
ADD COMMENTlink modified 2.4 years ago by Brian Bushnell15k • written 2.4 years ago by manekineko90
2
gravatar for Brian Bushnell
2.4 years ago by
Walnut Creek, USA
Brian Bushnell15k wrote:

"Mean inner distance between mate pairs = mean insert-size-2*read_length"

That is exactly correct.

So for a 2x100bp library with 193 mean insert, your inner distance is 193-2x100 = -7 (meaning that they overlap by 7bp).

ADD COMMENTlink written 2.4 years ago by Brian Bushnell15k

So I should use a negative -7 in Tophat (the default says it is 50)? is negative value ok?

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by manekineko90
1

It should be fine.  A negative inner distance is very common.  If it doesn't like -7 just use 0 which is close enough; it doesn't need to be exact.

ADD REPLYlink written 2.4 years ago by Brian Bushnell15k
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