User: predeus

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predeus1.1k
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Posts by predeus

<prev • 138 results • page 1 of 14 • next >
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Comment: C: samtools markdup vs PICARD's MarkDuplicates when removing duplicated reads
... Good call - like I said, "unless something has changed"! I agree, the results should be very comparable. ...
written 1 day ago by predeus1.1k
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Answer: A: samtools markdup vs PICARD's MarkDuplicates when removing duplicated reads
... Unless something has changed dramatically, you should use Picard and not samtools to mark duplicates in an aligned file. Even Heng Li (the author of samtools) said that he does not recommend using samtools markdup. The topic was discussed quite a lot, for example, here: http://seqanswers.com/forums/ ...
written 2 days ago by predeus1.1k
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Answer: A: Is there some good software to align/compare fasta sequences in my PC
... You can try Ugene - it's quite user-friendly and should do multiple sequence alignment and visualization. http://ugene.net/ ...
written 2 days ago by predeus1.1k
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Answer: A: Looking for the best plot for overlapping features
... So there's this tool that basically is used for interactive expression analysis: http://genome.ifmo.ru/phantasus-dev/ But you can use it to do heatmap-based visualization of nearly anything. Cluster your table using k-means and then sort by cluster. You should get a pretty good idea of feature ov ...
written 2 days ago by predeus1.1k
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Answer: A: How to circularize genome assemblies
... If you want to circularize the genome, I'd assume you are assembling a bacterial genome? If you have pacbio only, best assembler right now is Flye - it's very accurate, does not mess up the circularization, and generates quite nicely finished contigs If you have pacbio + illumina, Unicycler does ...
written 28 days ago by predeus1.1k
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Comment: C: Batch effect correction
... Yes, I meant you incorporate your "batch" variable into Deseq2 formula, and use NON-batch corrected data. Authors of comBat acknowledged that it might be over-correcting it that way. ...
written 6 weeks ago by predeus1.1k
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Comment: C: Is computing TPM from read count from DEseq2 count matrix necessary?
... why do you want to do it manually? Most modern quantification programs (featureCounts, rsem, kallisto, salmon) will do it for you. It's more complicated than just transcript length (and what is **mean** transcript length?) - the formula is > transcript length - mean fragment length + 1 (and ...
written 7 weeks ago by predeus1.1k
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Answer: A: When will the HG 19/ GRC37 finally become obsolete
... I'll go on a limb here and say that there is no clear benefit of switching from hg19 to hg38 for most purposes. So hg19 will become obsolete same time as hg38, when using graph-based genome reference will become feasible. ...
written 7 weeks ago by predeus1.1k
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Answer: A: which matrix should be used to draw heatmap in RNAseq?
... Depends on why do you need the visualization, right? Visualization can be done to explore the data, or to make a point in the publication etc If you want to explore the data, you can also try and specify for yourself, what exactly you want to find out - specific genes? Certain pathways? all this ma ...
written 7 weeks ago by predeus1.1k
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Comment: C: Interpretation of several pairwise overlaps
... I would look carefully into how you associate a particular feature with a gene name e.g. some genes are very long but, to answer your question, I think you are correct to assume that odds ratio would show the strength of association. ...
written 7 weeks ago by predeus1.1k

Latest awards to predeus

Appreciated 12 days ago, created a post with more than 5 votes. For C: How To Convert Gencode Gtf Into Bed Format ?
Good Question 12 days ago, asked a question that was upvoted at least 5 times. For Get a complete GSM-to-SRX/SRR table
Appreciated 7 weeks ago, created a post with more than 5 votes. For C: How To Convert Gencode Gtf Into Bed Format ?
Guru 7 weeks ago, received more than 100 upvotes.
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?
Scholar 7 weeks ago, created an answer that has been accepted. For A: Programs for bacterial gene prediction/annotation for nanopore assembly?
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?
Epic Question 3 months ago, created a question with more than 10,000 views. For Duplicates on Illumina
Popular Question 4 months ago, created a question with more than 1,000 views. For PCA and DE analysis for loop design microarray
Great Question 7 months ago, created a question with more than 5,000 views. For Duplicates on Illumina
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Librarian 8 months ago, created a post with more than 10 bookmarks. For Duplicates on Illumina
Popular Question 8 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 10 months ago, created a question with more than 1,000 views. For Classify Genes As Expressed Or Not Expressed
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Too late to switch to Bioinformatics?
Appreciated 14 months ago, created a post with more than 5 votes. For C: How To Convert Gencode Gtf Into Bed Format ?
Great Question 15 months ago, created a question with more than 5,000 views. For Duplicates on Illumina
Popular Question 17 months ago, created a question with more than 1,000 views. For Get a complete GSM-to-SRX/SRR table
Prophet 18 months ago, created a post with more than 20 followers. For Duplicates on Illumina
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