User: agata88

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agata88770
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Poland
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Posts by agata88

<prev • 345 results • page 1 of 35 • next >
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VarScan strand-filter in Ion Torrent output
... Hi all! I have VarScan mpileup2snp results: Only SNPs will be reported Min coverage: 3 Min reads2: 2 Min var freq: 0.1 Min avg qual: 15 P-value thresh: 0.05 7373346 bases in pileup file 3193 variant positions (841 SNP, 2352 indel) 1590 were failed by the strand- ...
ion torrent varscan written 6 days ago by agata88770
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Answer: A: are known polymorphisms in the primer sequence?
... In the meantime I found another solution: 1. Download common SNPs from here: common_all.vcf.gz (https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/) 2. Define primer coordinates in genome. 3. Run `samtools tabix common_all_vcf.gz chr:START-END` Best, Agata ...
written 24 days ago by agata88770
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Comment: C: are known polymorphisms in the primer sequence?
... Ok I see it, sorry! Thanks for suggestion! Best, Agata ...
written 24 days ago by agata88770
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Comment: C: are known polymorphisms in the primer sequence?
... I run In Silico PCR as you said, but I am not sure how can I concatenate the results with SNP tracks (dbSNP)? ...
written 24 days ago by agata88770
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Comment: C: are known polymorphisms in the primer sequence?
... Thanks! I will try that. ...
written 24 days ago by agata88770
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are known polymorphisms in the primer sequence?
... Hi all! How can I check whether primer sequence include know polymorphisms? I've read about snp blast, but it's seems no longer available: https://www.ncbi.nlm.nih.gov/SNP/snpblastByChr.html Thanks for any suggestions, Best, Agata ...
polymorphisms primer written 24 days ago by agata88770
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Answer: A: Variant calling in large sample populations
... You can try to follow this workflow: 1. Quality trimming - with Trimmomatic (http://www.usadellab.org/cms/?page=trimmomatic) 2. Mapping reads to human genome - with BWA (http://bio-bwa.sourceforge.net/) 3. Variant calling - with SAMtools mpileup (http://samtools.sourceforge.net/) or VarScan (http ...
written 24 days ago by agata88770
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Comment: 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 4 months ago by agata88770
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Comment: C: Primer design from bam file ?
... Corrected, thanks! Agata ...
written 4 months ago by agata88770
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Comment: 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 4 months ago by agata88770

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Popular Question 3 days ago, created a question with more than 1,000 views. For Trimming of 16S reads
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