User: predeus

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predeus540
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APredeus
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Posts by predeus

<prev • 81 results • page 2 of 9 • next >
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Comment: C: Modern software for whole genome alignment visualization
... Ah, thank you. This is very neat. ...
written 3 months ago by predeus540
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Comment: C: Modern software for whole genome alignment visualization
... ha, that is a very creative use of minimap2 :) at least there's a js visualization, worth a shot. Thank you. ...
written 3 months ago by predeus540
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Comment: C: Modern software for whole genome alignment visualization
... Last update on the code is in 2011, publications are from 2000-2004. Is it really still relevant? Visualizations look pretty horrible too (by modern standards of course). ...
written 3 months ago by predeus540
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Modern software for whole genome alignment visualization
... Hello all, I was wondering if there are any modern tools for visualization of whole-genome alignment, with ability to add annotation, and maybe extract variants? I've tried Mauve and Harvest so far, but they seem pretty abandoned and work quite poorly. Are there any modern projects you can recom ...
whole-genome alignment harvest visualization mauve written 3 months ago by predeus540 • updated 3 months ago by h.mon15k
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Answer: A: aligning with bacterial genome
... Bacterial RNA would hardly be detectable in human RNA-seq library - if you do poly-A selection, bacterial reads won't be there since there's almost no poly-A tails, and total RNA would still not capture bacterial RNA since they decay too fast (you need a special protocol for bacterial RNA-seq). Also ...
written 3 months ago by predeus540
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Answer: A: Snap aligner FASTQ record larger than buffer
... Snap beta 23 is available now - you can try upgrading and seeing if that would make your problem disappear. It seems that the program did not recognize that the files are gzipped, though. Try inflating them and running the program again. ...
written 3 months ago by predeus540
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Answer: A: What Is The Fastest Alignment Tool To Map Reads To A Big Genome Over 4Gb?
... I think it would be interesting to bump it up in 2018. What is the fastest aligners out there? I have heard (I think Heng Li wrote it somewhere) that with changes in computer architecture, hash-based aligners are coming to be more and more interesting, compared to FM-index based. I am about to try ...
written 3 months ago by predeus540
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Comment: C: Weird discrepancy of assigned reads in featureCounts when run on paired-end data
... Not quite everything. Lots of bacterial strand-specific RNA-seq is done using RNA ligation, and thus is -s 1. But you are right that most human/mouse/etc samples seem to be using dNTP strategy recently. ...
written 3 months ago by predeus540
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Answer: A: Get a complete GSM-to-SRX/SRR table
... Note that the table seems to be regularly updated - the most up-to-date file is now twice the size it was 11 months ago. ...
written 3 months ago by predeus540
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Answer: A: Protocols (workflow) for differential gene expression analysis of de novo assemb
... Most of the mentioned software tools are dramatically outdated - https://twitter.com/lpachter/status/937055346987712512?lang=en You have to solve one more problem than with normal differential expression analysis Normally, you want to 1) quantify the transcripts/genes; 2) do differential expressio ...
written 4 months ago by predeus540

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Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?
Appreciated 27 days ago, created a post with more than 5 votes. For C: How To Convert Gencode Gtf Into Bed Format ?
Great Question 8 weeks ago, created a question with more than 5,000 views. For Duplicates on Illumina
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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Popular Question 13 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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Popular Question 17 months ago, created a question with more than 1,000 views. For How To Determine If Library Is Strand-Specific
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Good Question 17 months ago, asked a question that was upvoted at least 5 times. For Duplicates on Illumina
Student 17 months ago, asked a question with at least 3 up-votes. For Duplicates on Illumina
Popular Question 2.1 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 2.5 years ago, created a question with more than 1,000 views. For Find All Annotated Rrna (Rdna) Sequences
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How To Determine If Library Is Strand-Specific
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