Determine inner mate distance and insert size of Pair end reads

Question

[Chirag Nepal]

Hi there,

I downloaded some pair-end exome data from SRA. I did not find info on inner mate distance and insert size for these data. Can someone please suggest me on how to get this information ?

Thanks for your help in advance !

Cheers

Answer 1

[Zev.Kronenberg]

Map the reads to the reference and look at the distribution of mate-pair mapping distances. Alternatively you could contact the authors to get the "true" distribution.

[st.ph.n]

After mapping there's a Picard tools command that will give you insert size metrics of a bam/sam file. You can map with bwa. Picard tools will output a histogram of the insert sizes.

[Chirag Nepal]

I mapped without insertsize parameter (default value) and use Picard to get insertsize.

I would have guessed to have a normal distribution of Insertsize length, but here we see it varying between 75-250.

What value (insertsize) might be the best for this? Any suggestions?

Thanks !