User: predeus

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predeus1.3k
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Posts by predeus

<prev • 154 results • page 1 of 16 • next >
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Comment: C: Modern software for whole genome alignment visualization
... Pretty much nothing outside things mentioned above. Dot is very good for large-scale comparison, and Artemis Comparison Tool (ACT) works nicely for detailed comparison using GFF annotation. ...
written 4 weeks ago by predeus1.3k
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Comment: C: optimise htseq count performance by choosing proper samtools sort options
... The BAM file still needs to be sorted, and AFAIK there are slightly different requirements for paired-end (fragment) and single-end (read) quantification. Basically, featureCounts will try to fix the mate pairs if it detects inconsistencies, but it's much slower than actual read counting, so it's be ...
written 6 weeks ago by predeus1.3k
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Answer: A: Tools for metagenomics classification using long reads
... It seems like MetaMaps should be quite good for this task. I'm about to test it with a couple of my datasets. ...
written 6 weeks ago by predeus1.3k
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Comment: C: A good tutorial for eukaryotic phylogeny?
... Thank you, that's an interesting approach. I need to compare quite distant species though, so I don't think alignment in nucleotide space would be very useful. ...
written 9 weeks ago by predeus1.3k
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A good tutorial for eukaryotic phylogeny?
... Hello all, I was wondering if you know of a good tutorial showing how to make a simple phylogeny of several eukaryotic species? Basically, as far as I understand, you start with an annotated genome, and need to 1) identify single-copy orthologues; 2) do multiple alignment; 3) select the "good" p ...
phylogeny tree eukaryote written 10 weeks ago by predeus1.3k • updated 9 weeks ago by Vitis2.3k
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Comment: A: Help scaffolding an Illumina genome assembly with 10x reads
... Did you gather any useful knowledge about the best way to use 10X reads? All the software I've tried seems to act up. ...
written 12 weeks ago by predeus1.3k
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Answer: A: Trinity RSEM Bowtie2 align_and_estimate_abundance script error
... Dir paths look kind of funny. Did you try running the commands mentioned in the debug manually? Try checking what "Trinity.fasta.bowtie2" actually is - is this a wrapper script? ...
written 5 months ago by predeus1.3k
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Answer: A: Sequence duplication levels in de-novo assemblies
... You probably would want to map the reads back to the assembly and then evaluate sequence duplication. FastQC works with raw reads and has limited power to inform you about the nature of your problems. If after paired-end mapping you still get high duplication rate, you probably are dealing with PC ...
written 5 months ago by predeus1.3k
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Answer: A: Principal Component Analysis PCA
... I'd also like to add that if 80% of variance in your 20-sample RNA-seq PCA is explained by PC1, there's either something very wrong with your samples, or with the way you are analyzing your data. Make sure they are log-transformed and normalized - ideally with something like vst or rlog transformati ...
written 5 months ago by predeus1.3k
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Comment: C: Principal Component Analysis PCA
... They must have only ran it on SNPs :) basically, the number of PCs = number of rows. Rows could be genes (for RNA-seq), SNPs, or anything else. ...
written 5 months ago by predeus1.3k

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Scholar 6 weeks ago, created an answer that has been accepted. For A: Programs for bacterial gene prediction/annotation for nanopore assembly?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Does any large resequencing project have a genuinely hg38 VCF?
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Does any large resequencing project have a genuinely hg38 VCF?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?
Great Question 3 months ago, created a question with more than 5,000 views. For How To Determine If Library Is Strand-Specific
Great Question 4 months ago, created a question with more than 5,000 views. For Find All Annotated Rrna (Rdna) Sequences
Popular Question 4 months ago, created a question with more than 1,000 views. For PCA and DE analysis for loop design microarray
Popular Question 4 months ago, created a question with more than 1,000 views. For PCA and DE analysis for loop design microarray
Prophet 5 months ago, created a post with more than 20 followers. For Modern software for whole genome alignment visualization
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For Get a complete GSM-to-SRX/SRR table
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Appreciated 6 months ago, created a post with more than 5 votes. For C: How To Convert Gencode Gtf Into Bed Format ?
Popular Question 7 months ago, created a question with more than 1,000 views. For PCA and DE analysis for loop design microarray
Appreciated 7 months ago, created a post with more than 5 votes. For C: How To Convert Gencode Gtf Into Bed Format ?
Good Question 7 months ago, asked a question that was upvoted at least 5 times. For Get a complete GSM-to-SRX/SRR table
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Guru 9 months ago, received more than 100 upvotes.
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?
Scholar 9 months ago, created an answer that has been accepted. For A: Programs for bacterial gene prediction/annotation for nanopore assembly?
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?
Epic Question 10 months ago, created a question with more than 10,000 views. For Duplicates on Illumina
Popular Question 12 months ago, created a question with more than 1,000 views. For PCA and DE analysis for loop design microarray
Great Question 14 months ago, created a question with more than 5,000 views. For Duplicates on Illumina

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