User: predeus

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predeus630
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630
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Russia
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http://bioinf.me/research
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APredeus
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3 hours ago
Joined:
5 years, 10 months ago
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Posts by predeus

<prev • 91 results • page 2 of 10 • next >
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Answer: A: Which software to use to map 100bp DNA sequence to genome
... Every time I see someone using Tophat or suggesting using it (unless you're dealing with colorspace RNA-seq) I cringe a little :) Bwa does better job estimating mapping quality, which is pretty important for variant calling. Otherwise, any genomic aligner that's well supported would do equally well. ...
written 3 months ago by predeus630
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Answer: A: STAR for chip-seq
... "too short" is STAR's euphemism for reads that just fail to align. What's the alignment rate you're getting with bowtie2? Chip-Seq is very tricky experimentally, so it happens quite often that libraries are full of adapter sequences etc. Aligners (as long as you are using a well-supported modern one ...
written 3 months ago by predeus630
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Comment: C: Racon-Illumina or Pilon?
... Very useful insight and link, thank you! The fact about many rounds of Pilon polishing is particularly interesting, since Unicycler (that performs exceptionally for hybrid bacterial assembly) does use this exact strategy (polishing with Pilon until convergence, i.e. there are no more changes happe ...
written 3 months ago by predeus630
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Racon-Illumina or Pilon?
... Hello all, I was experimenting with various options to improve Nanopore-based assembly by short reads (Illumina). It appears like there are options now to use Racon with Illumina, or to use Pilon. Does anybody know which one is better? Any other suggestions from experience? Thank you in adva ...
assembly polishing nanopore written 3 months ago by predeus630
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Huge jump in plasmid coverage - any idea why?
... Hello all, I am working on some bacterial genome assemblies that have been assembled using Pacbio reads only. I realized that I can make minor improvements to them (on the order of several SNPs and indels) by aligning Illumina data from the same strain to Pacbio assembly, and polishing it with Pil ...
pilon illumina bacteria pacbio written 6 months ago by predeus630
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Comment: C: Modern software for whole genome alignment visualization
... SNPs and indels with annotations (silent/missense/nonsense, frameshift/in-frame), for example. ...
written 6 months ago by predeus630
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Comment: C: Modern software for whole genome alignment visualization
... Maybe I did not make myself sufficiently clear. I have no problem choosing a classical genome browser (with one reference and one annotation) to view and analyze coverage, annotation, etc. Variant/coverage analysis for typical use cases (short reads aligned to a reference) are no problem as well. ...
written 6 months ago by predeus630
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Comment: C: Modern software for whole genome alignment visualization
... Artemis Comparison Tool (ACT) is the tool related to Artemis, that does multi-genome visualization. It's very ancient and bad though, just painfully so. Thank you for he anvi'o link, I will check it out though. ...
written 6 months ago by predeus630
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Comment: C: Modern software for whole genome alignment visualization
... yes, of course. I think I should have specified that I was looking for a dynamic visualization - sort of like genome browser, but for 2 (or possibly more) genomes. ...
written 6 months ago by predeus630
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Comment: C: Modern software for whole genome alignment visualization
... yes, I did mention it in the original post... it's very poorly maintained, it seems. And since it's a Java jar, if it fails, there's no real way to debug it - you just have to accept it. ...
written 6 months ago by predeus630

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Student 5 days ago, asked a question with at least 3 up-votes. For Duplicates on Illumina
Popular Question 15 days ago, created a question with more than 1,000 views. For Classify Genes As Expressed Or Not Expressed
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Great Question 5 months ago, created a question with more than 5,000 views. For Duplicates on Illumina
Popular Question 7 months ago, created a question with more than 1,000 views. For Get a complete GSM-to-SRX/SRR table
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Popular Question 16 months ago, created a question with more than 1,000 views. For Chip-Seq Of Conventional Tfs: What Are The Peaks W/O The Motif?
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Student 20 months ago, asked a question with at least 3 up-votes. For Duplicates on Illumina
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Chip-Seq Of Conventional Tfs: What Are The Peaks W/O The Motif?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Find All Annotated Rrna (Rdna) Sequences
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How To Determine If Library Is Strand-Specific
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