Hello,
I downloaded the data and did some tests.
The data does not assemble very well (I tried with k=25, I have
a job with k=19 running now).
It seems that a lot of
these sequences contain stretches of Ns
and I think that the k-mer length for this dataset has to be lowered.
*SRR125492_1.fastq.gz & SRR125492_2.fastq.gz
*
See http://www.ebi.ac.uk/ena/data/view/SRX000946
Those are the normal shotgun paired reads (180bp PCR Free Library)
Half of the reads don't even align on the reference (bwa+samtools+samstat).
Ray sees:
Peak 0
AverageOuterDistance: 161
StandardDeviation: 24
*SRR034527_1.fastq.gz & SRR034527_2.fastq.gz
*
See http://www.ebi.ac.uk/ena/data/view/SRX016062
"4kb Jumping Library"
A lot of sequences are just like this:
CGNNNNNNNNNNNNNNNNNNNCNNNNNNNNNNNNNNNNNNNNNTNNNNNNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNNNNNNGNNNNNNNNNNNNN
This will be useless.
Ray sees:
Peak 0
AverageOuterDistance: 236
StandardDeviation: 83
Peak 1
AverageOuterDistance: 3677
StandardDeviation: 209
*SRR034528_1.fastq.gz & SRR034528_2.fastq.gz
*
See http://www.ebi.ac.uk/ena/data/view/SRX016063
"4kb Jumping Library"
Ray detects:
Peak 0
AverageOuterDistance: 238
StandardDeviation: 84
Peak 1
AverageOuterDistance: 3676
StandardDeviation: 210
nikos ioannidis a écrit :
Hello,
I want to ask you about short jumping libraries,
if these libraries are genereted from the
Center of Allpaths Assembly Development the orientation is
<----- ---->
and are specially orientaed like this for alpaths,
so do I have to reverse them, because for example using Velvet
I have to reverse them in order to use them properly
a characteristic example of such a library is the rhodobacter 2.4.1
with fragment lib:
http://www.ebi.ac.uk/ena/data/view/SRX000946
and a set of jumping libs :
http://www.ebi.ac.uk/ena/data/view/SRX016062
http://www.ebi.ac.uk/ena/data/view/SRX016063
so in order to get the correct assembly with Ray should I reverse the
jumping libs and let the fragment libs as they are?
Thank you.
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