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User: agata88

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agata88 • 740
Reputation:
740
Status:
Trusted
Location:
Poland
Website:
http://bioidea.com.pl/en
Last seen:
19 hours ago
Joined:
3 years, 3 months ago
Email:
a***************@o2.pl

Posts by agata88

<prev • 334 results • page 1 of 34 • next >
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Comment: C: Removing contaminants from 16S data
... Thanks, This data is real and it has more reads in negative control. It's probably because of nested-PCR. I've decided to subtract reads. ...
written 18 days ago by agata88 • 740
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Removing contaminants from 16S data
... Hi all! I have one case sample and one negative control (water) with 16S fastq results. At the end of 16S analysis I have table with reads per sample and identified OTUs. Should I remove all OTUs represented in water from analysis or subtract reads? here is an example: water ...
16s written 19 days ago by agata88 • 740 • updated 19 days ago by WouterDeCoster ♦ 32k
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Comment: C: RNAseq computer source for TopHat and Cufflinks
... Yes I know, Thanks. ...
written 22 days ago by agata88 • 740
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Comment: C: RNAseq computer source for TopHat and Cufflinks
... Ok. Thanks. Do you know which approach will need less computer resources? ...
written 22 days ago by agata88 • 740
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Comment: C: RNAseq computer source for TopHat and Cufflinks
... What I should use instead? I used this approach few years ago and It did a good job. ...
written 22 days ago by agata88 • 740
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RNAseq computer source for TopHat and Cufflinks
... Hi all! I would like to ask about calculation specification for RNAseq analysis with TopHat2 and Cufflinks. I have 24 samples with ~20M of PE reads. The genome size is 6GB. Can anyone who have done similar analysis can give a hint how much computer resource I will need to run mapping with TopHat2 a ...
rnaseq cufflinks written 22 days ago by agata88 • 740 • updated 18 days ago by Charles Warden ♦ 5.5k
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Comment: C: Fill gaps in scaffolds
... Sanger, nice point! I forgot about multiplex. ...
written 5 weeks ago by agata88 • 740
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Comment: C: Fill gaps in scaffolds
... Please, Correct me if am wrong. I have 12 scaffolds, for each I designed two primers at the beginning (reverse) and at the end (forward). I need them to go outside sequence. Now, I have 24 starters. Since I don't know what is the scaffold orientation, I need to pair everyone with everyone and run PC ...
written 5 weeks ago by agata88 • 740
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Comment: C: Fill gaps in scaffolds
... yes, starters = primers ...
written 6 weeks ago by agata88 • 740
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Fill gaps in scaffolds
... Hi all! I have 12 scaffolds that need to be connected with Sanger PCR products. I would like to design starters for all sequences. Is there a tool that can do that automatically? I've tried CONTIGuator - it didn't help, cause my novel bacteria and it's related species reference sequence just don't ...
gaps scaffolds written 6 weeks ago by agata88 • 740

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