User: joneill4x

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joneill4x50
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Canada
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Posts by joneill4x

<prev • 29 results • page 1 of 3 • next >
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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 24 days ago by joneill4x50
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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 24 days ago by joneill4x50
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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 28 days ago by joneill4x50
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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 28 days ago by joneill4x50
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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 28 days ago by joneill4x50
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Displaying structural variants with JBrowse
... JBrowse supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with tabix), REST, and more file formats. If we can call large structural variants and record these calls in one of the file formats listed above, then in theory we should be able to display them via JBrowse. Can anyone recommend how t ...
genome visualization jbrowse written 28 days ago by joneill4x50 • updated 28 days ago by cmdcolin1.3k
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Finding non-polymorphic region of genome for PCR primer design
... I working with a highly heterozygous species. I want to find a region of the genome with no polymorphism. I am looking to design PCR primers as a positive control for a presence/absence marker. The PCR primers should amplify a non-polymorphic area of genome. The amplicon size should be 50-75 bp. ...
genome polymorphism pcr written 5 weeks ago by joneill4x50
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mutations causing predicted gene loss of function in healthy individual - WGS
... Just for interest, I had my whole genome re-seqeunced (BGISEQ-500, 30X coverage). Variants were called with GATK and the variants were annotated with SnpEff and annovar. SnpEff also predicted the functional effects of the variants. Interestingly, there are hundred of variants that are predicted c ...
genome sequencing annoation written 5 months ago by joneill4x50 • updated 5 months ago by Pierre Lindenbaum124k
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Answer: A: Align paired and unpaired reads simultaneously using Bowtie2?
... Like this: bowtie2 -x btInd -1 13_trimmed_R1.fastq.gz -2 13_trimmed_R2.fastq.gz -U 13_unpaired_1.fastq.gz,13_unpaired_2.fastq.gz -p 12 | samtools sort -@ 12 -T temp -o 13trimmed_sorted.bam Works for me. (bowtie2 version 2.3.2) ...
written 9 months ago by joneill4x50 • updated 9 months ago by ATpoint26k
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Comment: C: Figuring out HiC restriction enzyme
... Can you go into further detail how you figured it out gbdias? I am in the same situation as you were. There are 20 over-represented 7-mers located near the start of my reads. (Both for forward reads and reverse reads). How do I used this data to deduce the restriction enzyme cutting site? ...
written 15 months ago by joneill4x50

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