**190**wrote:

Hi all,

I have used Minia to assemble a contigs set from my paired end reads, as Minia instructed that it doesn't use pairing information for constructing assembly, then I continue to try SSPACE to exploit this pairing infomation from the SAME LIBRARY (which I have used to construct contigs set) for scaffolding. But after tried different parameters in SSPACE (k, a or parameters of lib.txt), it ALWAYS returns the scaffolded set exactly the SAME as initial contigs set. Did I miss something? Even if I didn't put the best parameters, I would be obtained a scaffold which might be somehow different from the initial contigs set, but here they are exactly the same.

Any suggestion is greatly welcomed, thanks a lot!

Here are my input and scaffolded summary:

my lib.txt:k71 bowtie 1.fastq 2.fastq 440 0.75 FRRequired inputs: -l = lib.txt Number of paired files = 1 -s = k71contigs.fasta -b = k71origin Optional inputs: -x = 0 -z = 0 -k = 10 -g = 0 -a = 0.7 -n = 10 -T = 16 -p = 1 READING READS k71: ------------------------------------------------------------ Total inserted pairs = 46314881 ------------------------------------------------------------ LIBRARY k71 STATS: ################################################################################ MAPPING READS TO CONTIGS: ------------------------------------------------------------ Number of single reads found on contigs = 6827738 Number of read-pairs used for pairing contigs / total pairs = 657371 / 657371 ------------------------------------------------------------ READ PAIRS STATS: Assembled pairs: 657371 (1314742 sequences) Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 440 +/-330): 645344 Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 9033 Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 0 --- Satisfied in distance/logic within a given contig pair (pre-scaffold): 2175 Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 819 --- Total satisfied: 647519 unsatisfied: 9852 Estimated insert size statistics (based on 645344 pairs): Mean insert size = 296 Median insert size = 248 REPEATS: Number of repeated edges = 0 ------------------------------------------------------------ ################################################################################SUMMARY: ------------------------------------------------------------ Inserted contig file; Total number of contigs = 882414 Sum (bp) = 762086901 Total number of N's = 0 Sum (bp) no N's = 762086901 GC Content = 38.49% Max contig size = 55233 Min contig size = 143 Average contig size = 863 N25 = 4488 N50 = 2157 N75 = 837 After scaffolding k71: Total number of scaffolds = 882414 Sum (bp) = 762086901 Total number of N's = 0 Sum (bp) no N's = 762086901 GC Content = 38.49% Max scaffold size = 55233 Min scaffold size = 143 Average scaffold size = 863 N25 = 4488 N50 = 2157 N75 = 837------------------------------------------------------------

**15k**• written 3.0 years ago by pbigbig •

**190**