I am having problems using SSPACE basic with my 454 paired-end data, and was hoping to get some help here. SSPACE runs fine using my Illumina PE data, but my 454-data has much longer insert-sizes (3-5 kb), and I think they really could make difference.

My problem is that SSPACE reads all the 454-pairs in, removes quite a lot of them as the include Ns, and then maps 0 of them. The report is below. It was difficult to get the reads in a format that SSPACE accepts, and I guess that the problem lies in the fastq-files. Some (very few) reads are too long (over 1024 bases), and bowtie complains about these. Would this crash the whole run? I know that bowtie is not the best choice for longer reads, but I thought it would still manage to map some reads? Is SSPACE premium the answer?

Any/all help would be much appreciated,

Henrik

READING READS Lib454:

------------------------------------------------------------

Total inserted pairs = 1217215

Number of pairs containing N's = 1066178

Remaining pairs = 151037

------------------------------------------------------------

...

LIBRARY Lib454 STATS:

################################################################################

MAPPING READS TO CONTIGS:

------------------------------------------------------------

Number of single reads found on contigs = 0

Number of pairs used for pairing contigs / total pairs = 0 / 0

------------------------------------------------------------

READ PAIRS STATS:

Assembled pairs: 0 (0 sequences)

Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 3709 +/-927.25): 0

Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 0

Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 0

---

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: 0

Estimated insert size statistics (based on 0 pairs):

Mean insert size = 0

Median insert size = 0

REPEATS:

Number of repeated edges = 0

------------------------------------------------------------

################################################################################

My problem is that SSPACE reads all the 454-pairs in, removes quite a lot of them as the include Ns, and then maps 0 of them. The report is below. It was difficult to get the reads in a format that SSPACE accepts, and I guess that the problem lies in the fastq-files. Some (very few) reads are too long (over 1024 bases), and bowtie complains about these. Would this crash the whole run? I know that bowtie is not the best choice for longer reads, but I thought it would still manage to map some reads? Is SSPACE premium the answer?

Any/all help would be much appreciated,

Henrik

READING READS Lib454:

------------------------------------------------------------

Total inserted pairs = 1217215

Number of pairs containing N's = 1066178

Remaining pairs = 151037

------------------------------------------------------------

...

LIBRARY Lib454 STATS:

################################################################################

MAPPING READS TO CONTIGS:

------------------------------------------------------------

Number of single reads found on contigs = 0

Number of pairs used for pairing contigs / total pairs = 0 / 0

------------------------------------------------------------

READ PAIRS STATS:

Assembled pairs: 0 (0 sequences)

Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 3709 +/-927.25): 0

Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 0

Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 0

---

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: 0

Estimated insert size statistics (based on 0 pairs):

Mean insert size = 0

Median insert size = 0

REPEATS:

Number of repeated edges = 0

------------------------------------------------------------

################################################################################

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