[mido1951]

if the merging is optional,
how to do overlap reads without merging the two files into one file??

[Brian Bushnell]

No, merging is optional.

[mido1951]

thanks for your answer.
So, the merging is necessary ??
thanks

[Brian Bushnell]

yes I know.
I'm talking of phase before getting contigs.
you know to make an assembly of reads that it must overlap.
In the case of paired end reads, how to find overlaps between the two files?
we F1.fq that contains reads RX.1 and F2.fq that contains reads RX.2.
how to find the overlap between these reads? is what we should do a merging between RX.1 and RX.2?
So the merging is necessary?
thanks

It's very simple. You do this:

bbmerge.sh in1=F1.fq in2=F2.fq out=merged.fq outu=unmerged.fq

[GenoMax]

@Rick/@OTU: In order to avoid a re-hash of things that have been already discussed in other threads I am posting two below.

http://seqanswers.com/forums/showthread.php?t=63703

http://seqanswers.com/forums/showthread.php?t=63571

@mido1951 is either mis-understanding some basic concepts about sequencing/assembly or I am not able to understand what @mid1951 wants to know.

[mido1951]

yes I know.
I'm talking of phase before getting contigs.
you know to make an assembly of reads that it must overlap.
In the case of paired end reads, how to find overlaps between the two files?
we F1.fq that contains reads RX.1 and F2.fq that contains reads RX.2.
how to find the overlap between these reads? is what we should do a merging between RX.1 and RX.2?
So the merging is necessary?
thanks

[westerman]

Use Panda or Flash (or probably a number of other programs) to do merging.

[OTU]

You realize that you are not doing this manually, right? You usually use a program, which creates overlapping/merging reads and gives you the contig.

[mido1951]

for example we have two fragments.
S1: ATCGTTGAGCAGACT and S2: TGAGCAGACTTAAGTAGTTTT they have an overlap zone"TGAGCAGACT". so the consensus is:ATCGTTGAGCAGACTTAAGTAGTTTT

we sequenced this two fragments S1 and S2 in paired end reads R1 and R2.
S1:R1: ATCGTTGAGCA
S1:R2: AGTCTGCTCAA (illumina read the fragment in the other way so I think that to write in reverse complement. correct me if I'm wrong)
S2:R1:TGAGCAGACTT
S2:R2:AAAACTACTTA (reverse complement)I think this way is built the R2.

how to make assembly in this case?

I speak of here. How the assembly in this case?
in both files (paired end), is what we must do the merging of the two files?

[OTU]

Sorry, you are right. I meant something different.
Your previous post depicts the assembly process correctly.
What I don't understand is what exactly is your question then?

[mido1951]

R2 reads are not in a form of reverse complement.

illumina read the fragment from the right.
so if S1 is read from right, is that we take the reverse complement fragment or fragment from the right?
In this case R2 is what?

[OTU]

R2 reads are not in a form of reverse complement.

[mido1951]

for example we have two fragments.
S1: ATCGTTGAGCAGACT and S2: TGAGCAGACTTAAGTAGTTTT they have an overlap zone"TGAGCAGACT". so the consensus is:ATCGTTGAGCAGACTTAAGTAGTTTT

we sequenced this two fragments S1 and S2 in paired end reads R1 and R2.
S1:R1: ATCGTTGAGCA
S1:R2: AGTCTGCTCAA (illumina read the fragment in the other way so I think that to write in reverse complement. correct me if I'm wrong)
S2:R1:TGAGCAGACTT
S2:R2:AAAACTACTTA (reverse complement)I think this way is built the R2.

how to make assembly in this case?

[OTU]

what example are you looking for?

[mido1951]

I know the operation of assembly programs.
but I basically want to understand the overlap between the paired end reads (the two files).
i have single cell not meta genome.
have you an example?