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Hey everyone,
I have a problem with Hgap.
The use of Hgap In SMRTPortal is fine. I run my data with this protocol (two 2 SMRTCells) and after this job has finished I want to open the metadata.rdf file to see the results of the sequencing.
BUT (here is my problem) I don't see the same results like with the protocol AlloraAssembly.
I can the the window part with the title “Genome: De Novo Assembly” - but there is no information about the number of contigs or the fine peak signs on the left and right side of each contig which shows me e.g the coverage.
The region window is empty except of the black-white-line in the upper part with informations about the length in Kb of this choosen contig.
The details windows doesn't look similar to the result of the AlloraAssembly as well but anyways here I have the possibility to see the number of matched reads, the bases in this contig and the coverage (x10; x20,...).
Does anyone have an idea why the presentation of my Hgap results differs that much from the AlloraAssembly result presentation in SMRTView? And how I might fixed this?
Or in generell... does your SMRTView presentation whith HGap also look like mine? Also a Yes or No would help to find out if this is normal or not ^^
Thanks a lot!
Btw I attached two snapShots from SMRTView (the left is with AlloraAsselmly and the right with HGap)
I have a problem with Hgap.
The use of Hgap In SMRTPortal is fine. I run my data with this protocol (two 2 SMRTCells) and after this job has finished I want to open the metadata.rdf file to see the results of the sequencing.
BUT (here is my problem) I don't see the same results like with the protocol AlloraAssembly.
I can the the window part with the title “Genome: De Novo Assembly” - but there is no information about the number of contigs or the fine peak signs on the left and right side of each contig which shows me e.g the coverage.
The region window is empty except of the black-white-line in the upper part with informations about the length in Kb of this choosen contig.
The details windows doesn't look similar to the result of the AlloraAssembly as well but anyways here I have the possibility to see the number of matched reads, the bases in this contig and the coverage (x10; x20,...).
Does anyone have an idea why the presentation of my Hgap results differs that much from the AlloraAssembly result presentation in SMRTView? And how I might fixed this?
Or in generell... does your SMRTView presentation whith HGap also look like mine? Also a Yes or No would help to find out if this is normal or not ^^
Thanks a lot!
Btw I attached two snapShots from SMRTView (the left is with AlloraAsselmly and the right with HGap)
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