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08252015, 05:40 PM  #1 
Junior Member
Location: Egypt Join Date: Apr 2014
Posts: 1

Scaffolding using SSPACE
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 :22832803 :outie :26 Code:
longjump : 76101 :3529535318 :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 readpairs 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 outofbounds): 0 Unsatisfied pairing logic within contigs (i.e. illogical pairing >>, << or <>): 356  Satisfied in distance/logic within a given contig pair (prescaffold): 0 Unsatisfied in distance within a given contig pair (i.e. calculated distances outofbounds): 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  Code:
lib2 bowtie longjump_1.fastq longjump_1.fastq 35000 0.2 FR 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 Thank you very much! Sara Last edited by Sara ElMetwally; 08252015 at 05:54 PM. Reason: fix grammer 
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