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Subset BAM file based on selected coverage, PacBio reads

arrow pbalign coverage bam pacbio written 22 days ago by MyrNat • 0

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164

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Minimum coverage for PacBio Arrow

assembly polishing pacbio arrow written 9 weeks ago by jean.elbers • 240

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247

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Arrow Assembly polishing Error "KeyError: 'BASECALLERVERSION'"

arrow pacbio basecallerversion assembly written 3 months ago by David_emir • 280 • updated 11 weeks ago by liu3yang • 0

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2.9k

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Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone

pbalign tutorial polishing pacbio arrow smrt limk written 9 months ago by Roxane Boyer • 560 • updated 4 months ago by elipow1 • 0

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711

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Problem installing quiver

quiver polishing pacbio arrow written 12 months ago by cristian • 90 • updated 8 months ago by johnj • 0

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Recent Replies

C: Does BWA mem ever discard or modify data by d-cameron • 1.8k
No matter what compressed storage format you use, the majority of the entropy in sequence data is...
C: Does BWA mem ever discard or modify data by d-cameron • 1.8k
>it can clip bases, you'll want to relax the defaults The bases are soft clipped so the infor...
C: How to run IGV by d-cameron • 1.8k
Run igv.bat from a command prompt to see the error message.
C: Questions about de novo genome assembly from mixed DNA samples by niuyw • 20
Thank you for your answer! It's very clear. Now I can proceed. Thank you :) I've got another que...
C: Does BWA mem ever edit data by e.benn • 0
Yes very good, I also need to keep the alignment, and the 'which pair-end' metadata, and probably...
C: FlexiDot: highly customizable, ambiguity-aware dotplots by toheitka • 170
Thank you a lot for saying this. It makes us happy, since we also love this tool.
C: Blastn Gives Different Results Based on Database Size by khv • 0
Thanks for the reply, this solved the issue
C: GNU parallel error: Command line too long by ole.tange • 3.0k
I have found no way to increase the execve limit.
C: Please suggest an appropriate genome-guided transcriptome assembler by seta • 980
Yes, here, biostar forum, I don't exactly remember why. However, I performed genome-guided transc...
C: Creating Interactive Volcano Plots with R and Plot.ly by steve • 1.5k
Not sure I understand the question, since the original post documents all the R code used in this...
C: the bam file used for Diffbind by jared.andrews07 • 730
Typically I leave them in, as many programs ignore them.
C: Please suggest an appropriate genome-guided transcriptome assembler by lieven.sterck • 1.6k
can you elaborate why some people advise to avoid them? Is > here the biostar forum btw?

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