Insert Length Estimated By Velvet

Question

[khikho]

As I read on the velvet manual

If the insert length of a library is unspecified, Velvet will attempt to measure it for us, based on the read-pairs which happen to map onto a common node.

So I leave the insert length blank but base on the same manual page it said

You should check the Velvet console output to make sure the insert length estimates are not absurd.

Where and How should I check the velvet insert length estimated!?

[bagdevi.mishra]

when I run velvetg without specifying insert length, the standard output captured in the nohup.out file contains the following lines. ......

[1564.566048] Computing read to node mapping array sizes

[1572.478116] Computing read to node mappings

[1593.435209] Estimating library insert lengths...

[1627.668440] Paired-end library 1 has length: 570, sample standard deviation: 43

[1634.073744] Paired-end library 2 has length: 244, sample standard deviation: 57

[1639.688635] Paired-end library 3 has length: 238, sample standard deviation: 54

Answer 1

[Istvan Albert]

if I recall this correctly there is a file in the Log folder that contains a copy of the console output, you will need to look at the contents of that file.

[Arun]

does the insert length here mean the inner distance between the pairs? or the TLEN parameter of the SAM file (meaning, the total length from the start of left most read to the end of right most read?

[khikho]

I check it but these are the only information which I have:

"Final graph has 32544 nodes and n50 of 53, max 748, total 428510, using 243620/110166607 reads"