User: agata88
agata88 • 790
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Posts by agata88
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... Hi all!
I am looking for free for academics tool for compound management. Something similar to Mosaic compound management software. I've found MScreen, but it seems to be outdated - I've found only publication.
Any suggestions?
Best,
Agata ...
written 5 weeks ago by
agata88 • 790
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... Write in terminal:
git clone https://github.com/GATB/minia.git
git clone https://github.com/jts/sga.git
Then go to cloned directories and follow installation instructions. ...
written 7 weeks ago by
agata88 • 790
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... How about ClustalO? - https://www.ebi.ac.uk/Tools/msa/clustalo/ ...
written 8 weeks ago by
agata88 • 790
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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 4 months ago by
agata88 • 790
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... Ok I see it, sorry! Thanks for suggestion! Best, Agata ...
written 4 months ago by
agata88 • 790
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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 4 months ago by
agata88 • 790
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... Thanks! I will try that. ...
written 4 months ago by
agata88 • 790
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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 4 months ago by
agata88 • 790
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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 4 months ago by
agata88 • 790
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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 8 months ago by
agata88 • 790
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