Hello,
after a PBJelly run I tried to validate some of the results manually.
I looked at some of the processed gaps in the "assembly" sub directories. For most of the closed gaps it was perfectly clear what PBJelly did. When just one PacBio read spanned a gab, I could easily find the inserted sequence in this read. When more reads spanned a gap I, could find the inserted sequence in the consensus sequence created by PBJelly most of the times. However, this was not always the case.
I found some examples where I was not able to identify the inserted sequence within the generated consensus sequence.
I created a pairwise alignment of the consensus sequence and the inserted sequence and found out that the inserted sequence is contained in the consensus sequence, but it is somehow divided in some parts.
Is there an explanation for this behavior?
Thanks for your help,
Kai
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Hello again,
today we found the answer to our question above:
In some cases the consensus sequence contained in "output.fasta" has another orientation than the reference sequence. In those cases the "FillSequence" in "fillingMetrics.json" can of course not be found one to one, because it is the reverse complement version of the sequence contained in the "output.fasta" file.
Sorry if I caused some confusion,
Kai
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Is it ok to keep the sequence in reverse complement mode in the new output.fasta or not?. How to deal with this behaviour? Is there a way to order the sequence as the original.fasta file?
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
Hello,
after a PBJelly run I tried to validate some of the results manually.
I looked at some of the processed gaps in the "assembly" sub directories. For most of the closed gaps it was perfectly clear what PBJelly did. When just one PacBio read spanned a gab, I could easily find the inserted sequence in this read. When more reads spanned a gap I, could find the inserted sequence in the consensus sequence created by PBJelly most of the times. However, this was not always the case.
I found some examples where I was not able to identify the inserted sequence within the generated consensus sequence.
I created a pairwise alignment of the consensus sequence and the inserted sequence and found out that the inserted sequence is contained in the consensus sequence, but it is somehow divided in some parts.
Is there an explanation for this behavior?
Thanks for your help,
Kai
Hello again,
today we found the answer to our question above:
In some cases the consensus sequence contained in "output.fasta" has another orientation than the reference sequence. In those cases the "FillSequence" in "fillingMetrics.json" can of course not be found one to one, because it is the reverse complement version of the sequence contained in the "output.fasta" file.
Sorry if I caused some confusion,
Kai
Is it ok to keep the sequence in reverse complement mode in the new output.fasta or not?. How to deal with this behaviour? Is there a way to order the sequence as the original.fasta file?