This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Determine inner mate distance and insert size of Pair end reads

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

exome paired-end bowtie
• 4,000 views • link
updated by Ram Ram • written by Chirag Nepal Chirag Nepal

1 answer

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.

• 1 views • link
updated by Ram Ram • written by Zev.Kronenberg Zev.Kronenberg

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.

• 0 views • link
written by st.ph.n st.ph.n

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.

< image not found >

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

Thanks !

< image not found >

• 0 views • link
updated by Ram Ram • written by Chirag Nepal Chirag Nepal

Log in to answer this question.

More posts like this