User: BioGeek
BioGeek • 130
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Posts by BioGeek
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... Is this possible to use long-reads in tadpole? ...
written 10 weeks ago by
BioGeek • 130
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... There are many mapper that uses ONT and PacBio flag separately. I always wonder why? Why not one flag for all kind of long reads? Is this to compensate error rate ? What if I corrected all reads before mapping ? Sorry for my ignorance, but I am curious about it. ...
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... Falcon were used to assemble the genome. After mapping, I notice such cases https://dazzlerblog.files.wordpress.com/2017/04/screen-shot-2017-04-18-at-9-54-01-am.png
I wanted to break the genome by those "error-some" regions (by middle of X and Y in the figure) and re-scaffold them. How to break the ...
written 11 weeks ago by
BioGeek • 130
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... How to break the assembled genome by error-some regions? I map ONT reads against the genome and it return many misaligned regions, how to break the genome into fragment on those regions ? ...
written 12 weeks ago by
BioGeek • 130
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... I am looking for a tool, that can along all the long reads against phased genome. I tried the traditional haploid mapper, but it split the reads due to very similar phased genome sequences. ...
written 4 months ago by
BioGeek • 130
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... mapping is done by minimap2 ...
written 7 months ago by
BioGeek • 130
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... I want to focus on all those reads that connect two or more contigs. How to extract ONLY those nanopore reads ? ...
written 7 months ago by
BioGeek • 130
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... from to value
1 VH1 JH1 88
2 VH3 JH1 273
3 VH4 JH1 10
4 VH5 JH1 0
5 VH6 JH1 0
6 VH1 JH2 43
7 VH3 JH2 113
8 VH4 JH2 153
9 VH5 JH2 0
10 VH6 JH2 50
11 VH1 JH3 226
12 VH3 JH3 432
13 VH4 JH ...
written 8 months ago by
BioGeek • 130
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... Thanks for the script.
I wanted to plot multiple hits scenarios, where single reference fragment/block is mapped to multiple locations in target.
As shown above, h1 fragments have multiple hits on q1 and q2.
I tried with your suggested script, but fail miserably :(
...
written 8 months ago by
BioGeek • 130
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8 follow
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... ![enter image description here][1]
How to Plot a circular overlapping plots, as shown in pic. ?
I tried following table to plot on http://mkweb.bcgsc.ca/tableviewer/
data C D
A 7 18
B 5 15
and it return http://mkweb.bcgsc.ca/tableviewer/tmp/fvufmlm/results/circos-table-fvufmlm-larg ...
written 8 months ago by
BioGeek • 130
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