Hello !
This is a good question and I have the answer for you.
Today is my collaboration day in my scheduling so I can provide
a detailed answer.
For Illumina data, you either have 2 files (*R1* and *R2* or *_1* and *_2*).
Both files have the same number of reads. The first file contains left
reads and
the second file contains right reads.
For Illumina paired-end sequencing, all reads are paired. This is just
simplier
and less confusing and this is basically possible because
the Illumina SBS sequencing technology uses reversible terminators.
The technology is described in reference 1.
You can also have a single file in case where single-end sequencing occured.
For 454 data, you will have 3 files for paired end sequencing (or
whatever it is called).
Mate pairs or paired reads with the 454 technology implies generating
libraries using
circularization and the biotin/streptavidin strategy. This is described
in reference 2.
As a consequence, a number of reads won't be paired,
these will just be plain & boring single-end reads.
The proportion of single-end reads in a paired end 454 run will vary.
The attributes
of the operator (mostly dexterity and intelligence as well as the level)
will make this proportion vary.
You will also obtain paired reads, obviously.
To explain to you and other readers, I downloaded the data you are using
from EBI.
I downloaded 3 454 files.
seb@fault:~/2012/454-$ ls -lh
total 29M
-rw-rw-r-- 1 seb seb 11M jun 1 10:24 SRR454996_1.fastq.gz
-rw-rw-r-- 1 seb seb 15M jun 1 10:24 SRR454996_2.fastq.gz
-rw-rw-r-- 1 seb seb 3,4M jun 1 10:24 SRR454996.fastq.gz
The EBI page erroneously reports that each of the three files has 92,871
sequences.
http://www.ebi.ac.uk/ena/data/view/SRP012081
The correct counts are:
seb@fault:~/2012/454-$ zcat SRR454996_1.fastq.gz|grep ^@SRR|wc -l
84448
seb@fault:~/2012/454-$ zcat SRR454996_2.fastq.gz|grep ^@SRR|wc -l
84448
seb@fault:~/2012/454-$ zcat SRR454996.fastq.gz|grep ^@SRR|wc -l
8423
There is 84448 * 2 sequences + 8423 sequences.
So you should use Ray with this:
mpiexec -n 64 \
Ray -k 25 -o SRP012081-Ray-Odin9 \
-p SRP012081/SRR454996_1.fastq.gz SRP012081/SRR454996_2.fastq.gz \
-s SRP012081/SRR454996.fastq.gz
> Also how can I understand if a library is shortjumpimg or longjumping?
On the EBI site, you have these columns too:
Library Name Library Layout Library Strategy Library Source Library
Selection
But they are not very informative regarding that.
This information may be available on EBI in the XML files, sometimes.
Your best chance for this information is usually the associated paper.
Ray will detect these for you anyway, or at least Ray will try.
For Neisseria meningitidis, everything should work quite well.
I think there are 3 standard sizes for 454 paired end sequencing:
* 3 kb
* 8 kb
* 20 kb
References
1. The paper describing the Illumina sequencing technology.
Nature. 2008 November 6; 456(7218): 53--59.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581791/?tool=pubmed
2. An application node describing 454 paired end sequencing
/Nature Methods/ - *5*, (2008) doi:10.1038/nmeth.f.212
http://www.nature.com/nmeth/journal/v5/n5/full/nmeth.f.212.html
Happy assembly.
nikos ioannidis a écrit :
Hello
I see that many studies at ENA have 454 GS FLX Titanium paired reads,
but most of the times the files are fastq1 fastq2 and fastq3
how should i compine these files as an input in Ray?
Like: -p fastq1 fastq2
-p fastq2 fastq3
something like that could work?
For example at this study : http://www.ebi.ac.uk/ena/data/view/SRP012081
they have:
Instrument Model Library Layout Run Read Count Run Base Count
Illumina HiSeq 2000 PAIRED 12,794,66
42Gb Fastq file#1
Illumina HiSeq 2000 PAIRED 12,794,66
42Gb Fastq file#2
454 GS FLX Titanium PAIRED 66,691
31Mb Fastq file#1<-
454 GS FLX Titanium PAIRED 66,691
31Mb Fastq file#2<-
454 GS FLX Titanium PAIRED 66,691
31Mb Fastq file#3<-
454 GS FLX Titanium PAIRED 92,871
39Mb Fastq file#1<-
454 GS FLX Titanium PAIRED 92,871
39Mb Fastq file#2<-
454 GS FLX Titanium PAIRED 92,871
39Mb Fastq file#3<-_
how should I set Ray for them?
Also how can I understand if a library is shortjumpimg or longjumping?
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