Thread: SSPACE help
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Old 10-18-2013, 06:41 AM   #4
boetsie
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Location: NL, Leiden

Join Date: Feb 2010
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The negative gap indicates a potential overlap between the two contigs. However, it seems unlikely that there is 615bp overlap between the contigs, indicating that the insert size you've provided in the library file is not correct.

To illustrate how this is estimated;

Say you have a two contigs, contig1 of 1000bp and contig2 of 2000bp, one of your paired-read aligns at position 900 at contig1 and the other at position 100 on contig 2.

If you set the insert size to 210bp, the estimated gap is;
Provided insert size - ((size of contig1)-(position of read1 on contig1)) + (position of read2 on contig2). In this case it is;
210 - (1000-900) + 100 = 10

So a gap of 10bp. If we change the insert size to 2000, it is;

2000 - (1000-900) + 100 = 1800

If we change the insert size to 100, it is;

100 - (1000-900) + 100 = -100

As you can see, the estimated gap really depends on the provided insert size by the user.

In your case I see a number of large negative gaps, this is highly unusual. Probably you should lower your insert-size by 600 bases.

Regards,
Boetsie
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