User: agata88
agata88 • 760
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Posts by agata88
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C: Primer design from bam file ?
... In case you don't want all SNPs, but only the unique for each sample, you can compare consensus linear sequences from 5 samples, and then design primers in desire places. Agata ...
written 5 weeks ago by
agata88 • 760
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C: Primer design from bam file ?
... Corrected, thanks! Agata ...
written 5 weeks ago by
agata88 • 760
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C: Primer design from bam file ?
... Consensus sequence is a linear sequence from bam file (mapped reads). For example, if you have sample reads mapped to reference genome, you can generate the linear representation of sequence for this sample. It will include all differ variants (SNPs). ...
written 5 weeks ago by
agata88 • 760
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C: Primer design from mapping file ?
... Just a suggestion: First, create consensus sequence from bam files for each sample (https://www.biostars.org/p/237833/ ). Design primers to your reference genome sequence (Primer3, https://www.ncbi.nlm.nih.gov/tools/primer-blast/ ), and then mach them to your consensuses, to see if they mach correct ...
written 5 weeks ago by
agata88 • 760
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... 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 10 weeks ago by
agata88 • 760
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... 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 ...
written 10 weeks ago by
agata88 • 760
• updated
10 weeks ago by
WouterDeCoster ♦ 35k
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... Yes I know, Thanks. ...
written 10 weeks ago by
agata88 • 760
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... Ok. Thanks. Do you know which approach will need less computer resources? ...
written 10 weeks ago by
agata88 • 760
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... What I should use instead? I used this approach few years ago and It did a good job. ...
written 10 weeks ago by
agata88 • 760
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... 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 ...
written 10 weeks ago by
agata88 • 760
• updated
10 weeks ago by
Charles Warden ♦ 5.8k
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