User: BioGeek

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BioGeek140
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Posts by BioGeek

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Comment: C: How to extract coordinate of hard and soft clipped long reads ?
... > RF01 567 576 RF01_508_1107_4:0:0_0:0:0_af I think these are longreads location! Is this possible to get reference chromosome/scaffold/contig location ? ...
written 6 weeks ago by BioGeek140
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Answer: A: Bioinformatics/Biotech Firms In India
... Here https://bioinformaticsonline.com/pages/view/1332/bioinformatics-companies-in-india ...
written 8 weeks ago by BioGeek140
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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 4 months ago by BioGeek140 • updated 4 months ago by Carambakaracho810
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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 6 months ago by BioGeek140
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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 6 months ago by BioGeek140 • updated 6 months ago by h.mon23k
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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 6 months ago by BioGeek140
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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 7 months ago by BioGeek140
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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 8 months ago by BioGeek140
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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 11 months ago by BioGeek140
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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 11 months ago by BioGeek140

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