chromosomer
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gtamazian
Assembled chromosome output
Hi gtamazian.
I followed your tutorial how to assembly the chromosome and it did rather smoothly. However when I checked the output file, I noticed the chromosome sequence was seperated by the Fragment identifier like
...TGGCTTGAA
>FRAGMENT2
CTCAGGGA...
Is this result okay?
Hello @quocviet0908 ,
Does your reference genome contain multiple chromosomes? It looks like the genome fragments were mapped to several chromosomes leading to more than one fragment in the produced assembly.
Yeah I followed your tutorial, the demo_chromosome.fa contains multiple chromosomes in that file. I also want to consult a another problem. My .fna file contains some scaffolds, but when I blasted them on the reference genome (Bacillus subtilis 168), every scaffold was split and return multiple hits which made me puzzled since I couldn't find the right gap value for the fragment map.
For instance, could you please download this .rar file and look into it? I extracted the sequence of the scaffold 17 and its blasted information in the excel file.
http://www.mediafire.com/file/ar92su98idt4yll/test_chromosomer.rar/file
It is quite normal that the alignments were split and you got multiple hits. According to the file that you attached, there is one high-score hit with the length of 610 bp, the identity of 99% and the bit score 1101. Its bit score surpasses the score of the next hit, that is 235, and Chromosomer will use the high-score hit as an anchor.
The gap value can be obtained by comparing sizes of assembled fragments and a reference genome. If we denote the total size of the assembled fragments by A and the total reference genome size by R, then the required gap size G can be obtained by the following equation:
G = |A - R|/(N - M)
where N is the number of the assembled fragments and M is the number of the reference chromosomes. In your case, R = 4,215,606 and M = 1.
Hi @gtamazian I'm appreciated for your help, I'll try to solve this with your guidance.