sebhtml/ray — Issue #43: Ray v1.7. Fails to produce scaffolds. Potential bug where PE-454 data with large inserts is not detected.
Author: mscook
Created: 2012-02-06 05:29:16+00:00
State: open

I believe this relates to: http://sourceforge.net/mailarchive/forum.php?thread_name=4F0F07C3.4070105%40ulaval.ca&forum_name=denovoassembler-users

454 PE-library information via newbler:

pairDistanceRangeUsed = 5108..15324
computedPairDistanceAvg = 10216.7
computedPairDistanceDev = 2554.2

Protocol
-----------

1) Use convert-sff.sh XXXX.sff (gives XXXX.sff.OUT.fastq.Forward.fastq XXXX.sff.OUT.fastq.Reverse.fastq and XXXX.sff.OUT.fastq.Single.fastq

2) Feed in ill-pe (previously interleaved and f/r/s 454 reads. Ray command:

ill=XXXX_proc.fastq
left=XXXX.sff.OUT.fastq.Forward.fastq
right=XXXX.sff.OUT.fastq.Reverse.fastq
single=XXXX.sff.OUT.fastq.Single.fastq

mpirun -np $NP Ray -p $left $right -i $ill -s $single -k 21 -o 21 -show-distance-summary

Output:
----------

Contigs.fasta
CoverageDistributionAnalysis.txt
CoverageDistribution.txt
degreeDistribution.txt
Library0.txt
Library1.txt
LibraryStatistics.txt
NetworkTest.txt
NumberOfSequences.txt
Rank(0-15).RayContigPaths.txt
RayCommand.txt
RayVersion.txt
SeedLengthDistribution.txt
SequencePartition.txt

LibraryStatistics:

LibraryNumber: 0
InputFormat: TwoFiles,Paired
DetectionType: Automatic
File: XXXX.sff.OUT.fastq.Forward.fastq
NumberOfSequences: 827693
File: XXXX.sff.OUT.fastq.Reverse.fastq
NumberOfSequences: 827693
Distribution: 17/Library0.txt

LibraryNumber: 1
InputFormat: Interleaved,Paired
DetectionType: Automatic
File: ec1810_proc.fastq
NumberOfSequences: 21689626
Distribution: 17/Library1.txt
Peak 0
AverageOuterDistance: 214
StandardDeviation: 59

It appears that the auto detection of peaks has failed for the 454 data.

Contents of Library0.txt:

253 1
273 1
423 1
425 1
433 1
449 1
1131 1
1409 1
2146 1

More to come when jobs are complete.