User: agata88

gravatar for agata88
agata88630
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630
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Location:
Poland
Website:
http://bioidea.com.pl/en
Last seen:
2 hours ago
Joined:
2 years, 4 months ago
Email:
a***************@o2.pl

Posts by agata88

<prev • 277 results • page 1 of 28 • next >
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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 12 days ago by agata88630
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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 12 days ago by agata88630
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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 12 days ago by agata88630
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Comment: C: a lot of OTUs wth no reference
... Thank you all for help. After considering your suggestions I've decided to push up to 100% OTU clustering for species discovery. I know that I will lost a lot of biological meaningful information but since I am curious only for species - I think this is the best option :) PS. I've checked 100% OTU ...
written 7 weeks ago by agata88630
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Comment: C: a lot of OTUs wth no reference
... This is the information I was looking for. Thanks. ...
written 7 weeks ago by agata88630
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Comment: C: a lot of OTUs wth no reference
... Yes, I think this is too much strict...if you have a good quality reads, and high number of reads you can assign taxonomy to species level even with 97% OTU clustering. ...
written 7 weeks ago by agata88630
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Comment: C: a lot of OTUs wth no reference
... Why 97% is to strict for soil samples? ...
written 7 weeks ago by agata88630
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Comment: C: a lot of OTUs wth no reference
... 97%, I've filtered singletons and doubletons. I am blasting against my own reference but the same results are for Geengenes (97_otu.fasta). I need to say that I am sure that this is not the software problem - because it was validated many times and worked very well . I am more curious about the ...
written 7 weeks ago by agata88630
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Comment: C: a lot of OTUs wth no reference
... I have my own taxonomy...but the same results are for Greengenes 97_otu.fasta. Taxonomy was unassigned at all. ...
written 7 weeks ago by agata88630
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a lot of OTUs wth no reference
... Hi all! I have more that 2000 OTUs detected, for which only 25% have assigned taxonomy. The quality of reads is good. I have suspicious that it is a soil sample but I am not sure about it. I know it's Miseq, V3-V4. After blast search of unassigned OTUs the results shows : "uncultured bacteria". ...
16s written 7 weeks ago by agata88630

Latest awards to agata88

Popular Question 18 days ago, created a question with more than 1,000 views. For normalization of NGS results
Popular Question 10 months ago, created a question with more than 1,000 views. For normalization of NGS results
Supporter 15 months ago, voted at least 25 times.
Centurion 15 months ago, created 100 posts.
Scholar 18 months ago, created an answer that has been accepted. For A: Idenity, e value or bitscore ?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Idenity, e value or bitscore ?
Scholar 20 months ago, created an answer that has been accepted. For A: Idenity, e value or bitscore ?

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