User: Lina F
Lina F • 120
- Reputation:
- 120
- Status:
- Trusted
- Location:
- Boston, MA
- Last seen:
- 2 months, 3 weeks ago
- Joined:
- 3 years, 7 months ago
- Email:
- l**********@gmail.com
Posts by Lina F
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... Yes, I have two de novo assemblies from long read data.
I actually also have Illumina data (I used it to error-correct the assemblies) but my main question here is what kind of differences exist between the two assemblies. ...
written 3 months ago by
Lina F • 120
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... I have tried Mauve and I agree, the scrolling is not great.
What kind of mapper would you recommend for calling SNPs, given that I have long contigs, not short Illumina reads? ...
written 3 months ago by
Lina F • 120
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... Hi all,
I de novo assembled two microbial strains of the same species into four contigs each. I assume they will be very similar in sequence, but I would like to know if there are SNPs or Indels.
I tried both mummer and Last to align the two genomes and I was able to generate dot plots, but they a ...
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... Great, thanks for pointing me in the right direction! ...
written 7 months ago by
Lina F • 120
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... 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 ...
written 7 months ago by
Lina F • 120
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... 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 7 months ago by
Lina F • 120
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... 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 ...
written 7 months ago by
Lina F • 120
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... 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 8 months ago by
Lina F • 120
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... 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 ...
written 8 months ago by
Lina F • 120
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... Great, thanks for the suggestion, I will take a look! ...
written 9 months ago by
Lina F • 120
Latest awards to Lina F
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