User: Macspider

gravatar for Macspider
Macspider580
Reputation:
580
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Trusted
Location:
Vienna - BOKU
Twitter:
macspider_music
Last seen:
5 days, 18 hours ago
Joined:
4 months, 2 weeks ago
Email:
r*********@gmail.com

Posts by Macspider

<prev • 127 results • page 1 of 13 • next >
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Answer: A: best way to interpret RNA-seq after counts and differential expression results?
... Read literature. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4728800/ ...
written 5 days ago by Macspider580
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Answer: A: Extract SNPs within 5 bps distance apart
... Yes, you can do it in many ways (python, command line, perl). You just have to ask for this condition to be verified: for each line, print line if (line_position - previous_line_position) <= 5 The position field in the VCF file is the 2nd :) https://samtools.github.io/hts-specs/VCFv4.2.pdf ...
written 6 days ago by Macspider580
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Answer: A: What are the compositional differences between Prokaryotes' gene/genome and Euka
... Hi Aritra, May I ask you if this is a homework question or something dealing with a project you're working on? Sounds like the first, but I hope I'm wrong. I have a trouble understanding what you mean. When you say: > Can I identify if a gene sequences is from prokaryotes or eukaryotes by anal ...
written 17 days ago by Macspider580
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Answer: A: large deletion detection in a haploid microbial eukaryote
... Pindel is what you are searching for: http://gmt.genome.wustl.edu/packages/pindel/ Be careful, it is *slow as hell*, so you might want to split your bam file into as many chunks as there are cores in your cluster. ...
written 17 days ago by Macspider580
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Comment: C: SNP Data Quality control
... As @Hasani pointed out, you shouldn't focus on the final number, because that tells you rather anything. For example, what happens if you divide it by the number of bases in the organism genome? Do you get a high mutation rate or one in the range? Other discussion point are: - how do you filter ...
written 18 days ago by Macspider580
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Comment: C: SNP Data Quality control
... I don't think @wouter wanted to know *who* gave you the data but rather *where* it comes from. For example: do you expect a lot of SNPs in a Breast cancer sample? (I would, but i'm not a breast cancer expert so this is just my guess). ...
written 18 days ago by Macspider580
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Comment: C: Progress bar to measure blast running time?
... I am not sure this is even feasible! It strongly depends on how many hits, the length of the HSPs, the dimension of the database, stuff like that... I don't think that you can "estimate" this. We're not capable to compute this in one line of code with the current soft- and hard-ware. :D How about c ...
written 18 days ago by Macspider580
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Comment: C: DESeq error of my data?
... Not a solution, but a suggestion: since your pipeline includes htseq as a counting algorithm, why don't you simplify your pipeline using the built-in function for htseq in DESeq2? DESeqDataSetFromHTSeqCount(sampleTable, directory = ".", design, ignoreRank = FALSE, ...) This will create a seqE ...
written 18 days ago by Macspider580
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Comment: C: Getting SNPs that are the complementary base of the reference
... @wouter @pierre thanks for the answers, I sorted it out after some plotting. All the reads mapping on the forward strand (which is T) had an A, so the whole read maps on the strand which should have a T at that position but has an A instead. Hence the SNP. Thanks anyway! ...
written 18 days ago by Macspider580
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Comment: C: Detecting Variants near repeats
... I stumbled on this post because I am struggling with some repetitive regions containing SNPs that bcftools calls. Given that obviously the tool cannot distinguish between a repetitive region and not, unless you tell it to do so, is it common practice to literally trim out SNPs in repetitive regions ...
written 18 days ago by Macspider580

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