Unfortunately, there are still some things unclear to me:
I understand the naming of the gaps in the gapinfo.bed file, but the other naming containing the 3' and 5' information is not completely clear to me.
So for example this name:
ref0001760.3e3
Does this mean that this is the 3' end of the 4th gap in the scaffold named ref0001760?
Is it true that the number after the point that is written in front of the e is just the number of the gap?
Would then ref0001760.0e5 be the beginning of the scaffold? Or ref0001760e5?
The assembly stage produces a file called masterSupport.bml which contains Lines looking like this:
Could you also please explain the liftOverTalbe.json a litte bit better?
Do the pluses and minuses corresponds to the original oritentations?
So for exaple this here: "Contig2566": [["ref0002104e3_ref0002104e5", "-", 13312]]
means that the original scaffold ref0002104 was inverted and is now called Contig2566 in the final version?
But what do all the numbers in the file mean?
And what is the meaning of "?" ?
If I want to find out which and how many Reads were used to fill a gap, which is the right file to look into? The assembly/masterSupport.bml file or support/my_file.fastq.gml? Or should I use an other file?
I'm very thankfull for any help!
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Hi there (:
I'm currently working myself through the PBjelly output to get more information what was done by the program. During my search, I found the following page: https://sourceforge.net/p/pb-jelly/wiki/PBJelly%20Output%20Tutorial/
Unfortunately, there are still some things unclear to me:
I understand the naming of the gaps in the gapinfo.bed file, but the other naming containing the 3' and 5' information is not completely clear to me.
So for example this name:
ref0001760.3e3
Does this mean that this is the 3' end of the 4th gap in the scaffold named ref0001760?
Is it true that the number after the point that is written in front of the e is just the number of the gap?
Would then ref0001760.0e5 be the beginning of the scaffold? Or ref0001760e5?
The assembly stage produces a file called masterSupport.bml which contains Lines looking like this:
What does these lines mean?
What does Nfill in the output.err file mean?
Could you also please explain the liftOverTalbe.json a litte bit better?
Do the pluses and minuses corresponds to the original oritentations?
So for exaple this here:
"Contig2566": [["ref0002104e3_ref0002104e5", "-", 13312]]means that the original scaffold ref0002104 was inverted and is now called Contig2566 in the final version?
But what do all the numbers in the file mean?
And what is the meaning of "?" ?
But what does this line tell me?
If I want to find out which and how many Reads were used to fill a gap, which is the right file to look into? The assembly/masterSupport.bml file or support/my_file.fastq.gml? Or should I use an other file?
I'm very thankfull for any help!