User: Lina F

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Lina F110
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Boston, MA
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Posts by Lina F

<prev • 73 results • page 1 of 8 • next >
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Comment: C: Removing common SNPs from a set of VCF files
... Great, thanks for pointing me in the right direction! ...
written 7 weeks ago by Lina F110
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Removing common SNPs from a set of VCF files
... Hi all, I am looking to generate a list of SNPs that are unique to different samples. To that end, I used bcftools to generate a list of common SNPs for each sample as follows: # for 9 samples bcftools isec -p intersection -n =9 *vcf.gz Now I am trying to subtract the common SNPs from th ...
vcf snp filtering written 7 weeks ago by Lina F110
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Comment: C: Ran dipSpades for a diploid fungus genome -- now what?
... Yes, my lab folks tell me it is considered to be a highly polymorphic diploid given dipSpades's definition ("haplomes that differ from each other by 0.4–10%".). Ultimately, I'm trying to get a somewhat reliable reference with phasing information. The final assembly should be about 16 megabases. I ...
written 9 weeks ago by Lina F110
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Ran dipSpades for a diploid fungus genome -- now what?
... Hi all, I successfully ran dipSpades for a diploid fungus genome but now I am feeling stuck on how to analyze the resulting output. I got the following results: consensus_contigs.fasta -> 300 contigs paired_consensus_contigs.fasta -> 216 contigs unpaired_consensus_contigs.fasta ...
dipspades diploid genome assembly written 9 weeks ago by Lina F110
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Comment: C: How to filter SNPs after Freebayes, if at all, in a fungal haploid genome alignm
... I have >100X coverage, so I should be ok on that front. I will take a look at IGV. Ultimately, I would like to script this pipeline so that I don't have to look at all genomes manually but maybe there is no way around that. ...
written 12 weeks ago by Lina F110
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How to filter SNPs after Freebayes, if at all, in a fungal haploid genome alignment?
... Hi all, I aligned Illumina reads of a haploid fungal genome against a reference sequence and then called SNPs with Freebayes: /home/ubuntu/freebayes/bin/freebayes -f reference.fasta alignment.bam --ploidy=1 --min-alternate-qsum 30 -F 0.05 > snps.vcf I then followed [this tutorial][1] to fi ...
freebayes snp filtering written 12 weeks ago by Lina F110
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Comment: C: Align two microbial genomes -- is mummer still the way to go?
... Great, thanks for the suggestion, I will take a look! ...
written 3 months ago by Lina F110
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Align two microbial genomes -- is mummer still the way to go?
... Hi all, I have assemblies of two microbial genomes from PacBio data (49 and 69 contigs each) and I'm trying to figure out how similar they are. The final genome size should be about 7.5 Mb. I remembered the mummer tools from a project many years ago, so I ran nucmer and got the SNPs output using s ...
vcf genome alignment mummer snps nucmer written 3 months ago by Lina F110
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Comment: C: Duplicates on Illumina
... One NextSeq was new, I believe, in March 2016 and we just got a second one 1-2 months ago that was used. Not sure exactly how old that one is (I will try and find out) ...
written 3 months ago by Lina F110
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Comment: C: Duplicates on Illumina
... I also just confirmed with the lab that both of our NextSeqs are NextSeq 500 and we use RTA V2 for basecalling. ...
written 3 months ago by Lina F110

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