Hi All,

I would like to do scaffolding using short and long jump libraries from GAGE website for Human Ch 14 using my own created contigs for the same data set.

the details of the Data Set and libraries are:

Original reads(Chr14):

Code:

: readLen :insLen :orientation :readCvg

Code:

frag : 101 :155 :innie : 42

Code:

shortjump : 101 :2283-2803 :outie :26

Code:

longjump : 76-101 :35295-35318 :innie :1.3

I would like to compare my results if I am using short, long jump or both libraries. I did scaffolding using short jump library and the problem when I am using long jump library, I found that SSPACE did not do scaffolding.

When I check the scaffold summary file, I found:

Code:

READING READS lib2:
------------------------------------------------------------
Total inserted pairs = 1202532
------------------------------------------------------------
LIBRARY lib2 STATS:
################################################################################
MAPPING READS TO CONTIGS:
------------------------------------------------------------
Number of single reads found on contigs = 2490
Number of read-pairs used for pairing contigs / total pairs = 356 / 1245
------------------------------------------------------------
READ PAIRS STATS:
Assembled pairs: 356 (712 sequences)
Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 35000 +/-7000): 0
Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 0
Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 356
---
Satisfied in distance/logic within a given contig pair (pre-scaffold): 0
Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 0
---
Total satisfied: 0 unsatisfied: 356
Estimated insert size statistics (based on 0 pairs):
Mean insert size = 0
Median insert size = 0
REPEATS:
Number of repeated edges = 0
------------------------------------------------------------
################################################################################
################################################################################
SUMMARY:
------------------------------------------------------------
Inserted contig file;
Total number of contigs = 70469
Sum (bp) = 87778699
Total number of N's = 0
Sum (bp) no N's = 87778699
GC Content = 40.82%
Max contig size = 47457
Min contig size = 115
Average contig size = 1245
N25 = 5909
N50 = 3142
N75 = 1483
After scaffolding lib2:
Total number of scaffolds = 70469
Sum (bp) = 87778699
Total number of N's = 0
Sum (bp) no N's = 87778699
GC Content = 40.82%
Max scaffold size = 47457
Min scaffold size = 115
Average scaffold size = 1245
N25 = 5909
N50 = 3142
N75 = 1483
------------------------------------------------------------

my Library.txt file is :

Code:

lib2 bowtie longjump_1.fastq longjump_1.fastq 35000 0.2 FR

and the SSPACE command line is:

Code:

./SSPACE_Standard_v3.0.pl -l long_lib.txt -s H.contigs.fasta -x 0 -m 32 -o 20 -k 5 -a 0.70 -n 15 -p 0 -v 0 -z 0 -g 0 -T 1 -S 0 -b SSPACE_H_long

I apprciate If someone help me to figure out what is the problem with long jump library.

Thank you very much!

Sara