User: agata88
agata88 • 660
- Reputation:
- 660
- Status:
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- Location:
- Poland
- Website:
- http://bioidea.com.pl/en
- Last seen:
- 2 days, 3 hours ago
- Joined:
- 2 years, 11 months ago
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Posts by agata88
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... 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% ...
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... to show significant difference at p< 0,05. ...
written 3 months ago by
agata88 • 660
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... 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
agata88 • 660
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... 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
agata88 • 660
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... 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 ...
written 3 months ago by
agata88 • 660
• updated
3 months ago by
Pierre Lindenbaum ♦ 108k
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... 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
agata88 • 660
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... Thanks a lot! Best, Agata ...
written 4 months ago by
agata88 • 660
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... 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
agata88 • 660
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... 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
agata88 • 660
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... 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 ...
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