User: predeus

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predeus860
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Russia
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http://bioinf.me/research
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APredeus
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Posts by predeus

<prev • 111 results • page 1 of 12 • next >
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Answer: A: Is There A Tool To Visualize Sequence Graphs?
... And now there's also AGB: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btz072/5306331 ...
written 8 days ago by predeus860
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Comment: C: STAR for bacterial genome
... I think the formula might be over-estimating the value a bit. The number min(14, log2(GenomeLength)/2 - 1) for something like Ecoli/Salmonella should be approximately 10, yet sometimes I get segfaults with this setting. Changing it to 8 fixes everything. ...
written 24 days ago by predeus860
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Comment: C: STAR for bacterial genome
... I've made quite a few comparisons, but haven't published them yet. Briefly, bacterial genomes are quite easy to map to - so uniquely mapped reads don't differ much between bwa/bowtie2/STAR/etc. However STAR/hisat2 are a lot better in reporting multimappers, which could be interesting for highly re ...
written 24 days ago by predeus860
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Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... Sorry, but I don't understand your arguments.. The main difference for well established genomes and transcriptomes would be speed. And Tophat2 is so, so slow. As far as other things you mentioned, 1) In STAR, you can provide GTF file when generating reference, so when if you really want that known ...
written 7 weeks ago by predeus860
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Comment: C: Best RNA-Seq aligner: A comparison of mapping tools
... Authors of Tophat begged to stop using it. It's a very outdated tool. https://twitter.com/lpachter/status/937055346987712512?lang=en ...
written 8 weeks ago by predeus860
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Comment: C: Using Bandage to finish ambiguous long-read assembly?
... yes, I've ran it with my data and it worked very well (I've ran it against Illumina reads). ...
written 9 weeks ago by predeus860
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Comment: C: Using Bandage to finish ambiguous long-read assembly?
... I have just a few contigs - the assembly is almost complete. ...
written 10 weeks ago by predeus860
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Comment: C: Using Bandage to finish ambiguous long-read assembly?
... As a matter fact I do have some Illumina! Thank you, very good suggestion. ...
written 10 weeks ago by predeus860
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Using Bandage to finish ambiguous long-read assembly?
... Hello all, I have a Unicycler assembly of a bacterial genome from PacBio and Illumina reads. It's a rather small but repetitive genome, and it's didn't assemble into one circualr chromosome, despite having 500x long read coverage. I've tried few other options (i.e. long read-only assemblers) and ...
unicycler assembly long reads bandage written 3 months ago by predeus860 • updated 6 weeks ago by Biostar ♦♦ 20
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Comment: C: How Can I Convert Bam/Sam To Wiggle
... Here's something interesting about this solution: **samtools depth has an arbitrary cutoff of 8000!** Anything above that is just discarded. I have no idea why was it made default, and still kind of cannot believe it. If you want your wig file to report true coverage from the BAM file, you would hav ...
written 3 months ago by predeus860

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Popular Question 24 days ago, created a question with more than 1,000 views. For PCA and DE analysis for loop design microarray
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Popular Question 4 months ago, created a question with more than 1,000 views. For Get a complete GSM-to-SRX/SRR table
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