User: joneill4x

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joneill4x100
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Posts by joneill4x

<prev • 34 results • page 1 of 4 • next >
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Comment: C: targeted RNA-Seq best practices
... Thank you for your reply. I was thinking about something like the following, but I will look into qPCR. Please direct me to any good tutorials if you know of them. Thanks again. https://www.illumina.com/techniques/sequencing/rna-sequencing/targeted-rna-seq.html "Targeted Amplicon RNA-Seq" "Prov ...
written 7 weeks ago by joneill4x100
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targeted RNA-Seq best practices
... What are the best practices for a targeted RNA-Seq experiment? (GOAL: Test if a specific list genes are differentially expressed in sample1 vs. Sample 2) How to design the primers that capture the target genes? Whats sort of controls are necessary, if any? Thank you. ...
primers experimental design rna-seq written 7 weeks ago by joneill4x100 • updated 7 weeks ago by ivivek_ngs5.0k
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Answer: A: Displaying structural variants with JBrowse
... I used Manta and paftools to call structural variants and store them in a VCF format, which was displayed in JBrowse. For Manta, I had to filter the VCF file to keep only variants with 'PASS'. ...
written 4 months ago by joneill4x100
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Comment: C: Picard MarkDuplicates tool on a pooled sample BAM
... Sorry, my mistake. I meant to ask: Would the Picard MarkDuplicates tool be acceptable to use on a pooled sample BAM file?(Multiple diploid samples have their DNA extracted, the DNA is pooled together, then the pool of DNA is sequenced). Or is it meant only for a single diploid sample? ...
written 7 months ago by joneill4x100
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Picard MarkDuplicates tool on a pooled sample BAM
... Would the Picard MarkDuplicates tool be acceptable to use on a pooled sample BAM file? (Multiple diploid samples have their DNA extracted, the DNA is pooled together, then the pool of DNA is sequenced) Or is it meant only for a single diploid sample? Thank you. ...
illumina picard markduplicates written 7 months ago by joneill4x100
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Comment: C: Low mean of read depth - filtering SNP in VCF file
... GT:AD:DP:**GQ**:PGT:PID:PL The GQ field is the genotype quality score. It is a value on the Phred scale. A GQ score of 20 means that there is a 1% chance that GT value is erroneous. A GQ score of 30 means that there is a 0.1% chance that the GT value is erroneous. See https://drive5.com/usearch/ ...
written 10 months ago by joneill4x100
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Answer: A: MUMmer aligments: How to visualize better the plots?
... Genome Ribbon http://genomeribbon.com/ https://youtu.be/Ih4Wf2U10-4 D-GENIES usues minimap2 rather than MUMmer. I have found it extremely useful. http://dgenies.toulouse.inra.fr/run ...
written 10 months ago by joneill4x100
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Comment: C: Displaying structural variants with JBrowse
... I am very interested. Please let me know how I can get involved. I guess that means I should hurry up and figure out how to call the structural variants and store them in a VCF! Thanks cmdcolin. ...
written 10 months ago by joneill4x100
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Comment: C: Low mean of read depth - filtering SNP in VCF file
... The HaplotypeCaller step does local re-alignment, which increases the quality of the variant calls. You can use vcftools to filter a VCF file on minimum genotype quality score. Example: vcftools --vcf firstTomatoGBS_filt_v2.5.vcf --minGQ 20 --max-missing 0.05 --maf 0.01 --recode --out qualFilt ...
written 10 months ago by joneill4x100
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Answer: A: Low mean of read depth - filtering SNP in VCF file
... I would recommend processing your data with GATK and follow their best practices. Since your species is cattle, you will 'hard-filter' the variant calls. https://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set Once GATK has output the final, hard-filtere ...
written 10 months ago by joneill4x100

Latest awards to joneill4x

Supporter 7 weeks ago, voted at least 25 times.
Scholar 5 months ago, created an answer that has been accepted. For A: MUMmer aligments: How to visualize better the plots?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Detecting gene duplication in de-novo assembly
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Detecting gene duplication in de-novo assembly
Popular Question 3.4 years ago, created a question with more than 1,000 views. For De novo genome assembly strategy
Popular Question 4.0 years ago, created a question with more than 1,000 views. For De novo genome assembly strategy

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