User: agata88

gravatar for agata88
agata88660
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Poland
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http://bioidea.com.pl/en
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2 days, 3 hours ago
Joined:
2 years, 11 months ago
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Posts by agata88

<prev • 284 results • page 1 of 29 • next >
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HMP database, how to process 16S data?
... Hi all! Lately I was processing some public 16S data and I came across Human Microbiom Project. I've decided to train on this data. For this purpose I downloaded SRR files (16S raw sequences) for elbow body site, you can see this here: https://portal.hmpdacc.org/search/c?filters=%7B%22op%22:%22and% ...
hmp 16s 454 written 8 weeks ago by agata88660 • updated 5 weeks ago by Biostar ♦♦ 20
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Comment: C: Comparison of SNPs between groups of samples
... to show significant difference at p< 0,05. ...
written 3 months ago by agata88660
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Comment: C: Comparison of SNPs between groups of samples
... I would like to see whether there are variants that occur only in sick patients and not in healthy group. In addition, I would like to see that in multiple samples comparison. For example, let's say I've found 5 mutations that occur in 20 sick samples and not occur in healthy group at all - this 5 m ...
written 3 months ago by agata88660
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Comment: C: Comparison of SNPs between groups of samples
... Thanks, it's one way. I'am thinking about something different. What is on my mind is to go back to variant detection step and use VarScan Somatic caller. I might use samtools mpileup to generate two vcf's each containing variants for 30 samples. Do you think it's good idea? ...
written 3 months ago by agata88660
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Comparison of SNPs between groups of samples
... Hi all! Could you please recommend a tool that can statistically compare SNPs between two groups of vcf's? To be more clear, I have 30 vcf files for healthy patients, and 30 for sick patients. I need to search for some kind of SNP patterns, statistically significant between those two groups. Any ...
snp written 3 months ago by agata88660 • updated 3 months ago by Pierre Lindenbaum108k
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Answer: A: how would I find SNPs that are highly polymorphic between populations in dbSNP
... This may help: https://www.biostars.org/p/72498/ You can download dbSNP database in vcf file and try vcftools to select those SNP of your interest. Best, Agata ...
written 3 months ago by agata88660
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Comment: C: How can I predict the time of calculations for RNAseq?
... Thanks a lot! Best, Agata ...
written 4 months ago by agata88660
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Comment: C: How can I predict the time of calculations for RNAseq?
... Woow, I am surprised. Last year I was performing RNAseq analysis withe the use of TopHat and Cufflinks and the results was fine. I was going to repeat that pipeline this year. Thanks for letting me know. I will go with other solutions. ...
written 6 months ago by agata88660
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Comment: C: How can I predict the time of calculations for RNAseq?
... I have 12 samples. Thanks for tips. Although I am flexible with time I would like to do it wisely. ...
written 6 months ago by agata88660
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How can I predict the time of calculations for RNAseq?
... Hi all! I am going to have PE reads for human RNAseq (around 70 millions of reads). How can I predict whether my computer have enough disc space and memory to run mapping reads to reference genome with the use of TopHat or any other RNAseq mapping algorithm? I would like to decide whether I need t ...
rna-seq written 6 months ago by agata88660 • updated 4 months ago by arup340

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Popular Question 25 days ago, created a question with more than 1,000 views. For alpha-diversity beta-diversity rarefaction curves
Popular Question 4 weeks ago, created a question with more than 1,000 views. For alpha-diversity beta-diversity rarefaction curves
Popular Question 5 weeks ago, created a question with more than 1,000 views. For SNPEff, SNPSift errors
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