User: BioGeek

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BioGeek130
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Posts by BioGeek

<prev • 37 results • page 1 of 4 • next >
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How to extract coordinate of hard and soft clipped long reads ?
... I wanted to extract the genome coordinate of all those location where longreads are soft/hard clipped. Genome ] [ __________________________________________________________________________________ --- ----------------------- ------------------------------- ...
clipped longreads mapping bam written 6 weeks ago by BioGeek130 • updated 6 weeks ago by Carambakaracho620
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Comment: C: Extending ends of sequences with the help of reads?
... Is this possible to use long-reads in tadpole? ...
written 4 months ago by BioGeek130
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PacBio and ONT reads difference !
... 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. ...
reads nanopore pacbio written 4 months ago by BioGeek130 • updated 4 months ago by h.mon21k
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Comment: C: Break the assembled genome by error-some regions !
... 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 4 months ago by BioGeek130
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Break the assembled genome by error-some regions !
... 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 ? ...
genome assembly breaks error ont written 4 months ago by BioGeek130
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Is there any mapper to map the long/short reads against phased genome?
... 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. ...
reads alignment mapper longreads phased written 5 months ago by BioGeek130
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Comment: C: How to extract all ONT reads that connect/overlaps two or more contigs ?
... mapping is done by minimap2 ...
written 9 months ago by BioGeek130
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How to extract all ONT reads that connect/overlaps two or more contigs ?
... I want to focus on all those reads that connect two or more contigs. How to extract ONLY those nanopore reads ? ...
reads nanopore scaffolding overlaps written 9 months ago by BioGeek130
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Comment: C: How to plot overlapping fragments in Circos ?
... 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 10 months ago by BioGeek130
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Answer: A: How to plot overlapping fragments in Circos ?
... 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 10 months ago by BioGeek130

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