User: a.m.dekker

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a.m.dekker0
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Posts by a.m.dekker

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Answer: A: PacBIO LAA barcoding problems
... What I noticed is that I was using smrtlink v6, whereas the subreads.bam file had a header saying it was created in smrtlink v5. Smrtlink v6 does not have tools to barcode subreads.bam files, thus I suspect this is not necessary in this version. For example, V6 already has a builtin feature before ...
written 9 weeks ago by a.m.dekker0
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PacBIO LAA barcoding problems
... Dear all, I have a question regarding the PACBio smrtlink (V. 6.0.0.47841) long amplicon analysis (LAA) on an externally performed PACBio Sequel sequencing run (of which, unfortunately, we don't have any upstream information). Our research involves pooled samples that were barcoded symetrically. An ...
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Comment: C: Phylogenetic tree for pooled PACBio sequencing material
... Thank you for your suggestion! Your link shows me how to preprocess my pacbio data for clustering raw reads for creating consensus reads (which is already done in my case), is that correct? I am looking for an algorithm suitable to cluster these consensus long amplicons for sample analysis. ...
written 9 months ago by a.m.dekker0
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Comment: C: Phylogenetic tree for pooled PACBio sequencing material
... Thank you for your question, I should be more clear. Yes, basically by visual inspection. I am indeed working with amplicons and trying to visualize variation in one gene between different samples of a plant species (I thus assume homology, yes). I decided that my tree is sloppy, because from some/m ...
written 9 months ago by a.m.dekker0
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Phylogenetic tree for pooled PACBio sequencing material
... Dear everybody! I have a question regarding building phylogenetic trees. I am working with pooled (n = ~ 500) PACBio sequencing material with reads of ~ 4kb length. I am not very familiar with the current methods for building trees, so was wondering whether someone could help me out! I tried clusta ...
phylogeny pooled msa pacbio written 9 months ago by a.m.dekker0 • updated 7 months ago by Biostar ♦♦ 20
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Comment: C: Does vcf-consensus support indels?
... Sorry guys, I figured it out. My problem was caused by the difference of indel representing by BBMap. I now call BBMap using sam=1.3 and for bcftools I use call -m (multiallelic) Figured it out using: http://seqanswers.com/forums/showthread.php?t=61535 ...
written 11 months ago by a.m.dekker0
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Comment: C: Does vcf-consensus support indels?
... Hi! For some reason when I try bcf consensus, indels are not taken into account. When i do samtools mpileup and bcftools call to create a vcf file, it will annotate indels but with a 0/0 genotype. I think that has to do with bcftools consensus not including indels it in the consensus seq. Have you n ...
written 11 months ago by a.m.dekker0

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Scholar 9 weeks ago, created an answer that has been accepted. For A: PacBIO LAA barcoding problems

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