User: agata88
agata88 • 770
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Posts by agata88
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... 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- ...
written 6 days ago by
agata88 • 770
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... 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
agata88 • 770
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... Ok I see it, sorry! Thanks for suggestion! Best, Agata ...
written 24 days ago by
agata88 • 770
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... 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
agata88 • 770
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... Thanks! I will try that. ...
written 24 days ago by
agata88 • 770
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... 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 ...
written 24 days ago by
agata88 • 770
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... 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
agata88 • 770
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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
agata88 • 770
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Comment:
C: Primer design from bam file ?
... Corrected, thanks! Agata ...
written 4 months ago by
agata88 • 770
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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
agata88 • 770
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