User: Lina F

gravatar for Lina F
Lina F110
Reputation:
110
Status:
Trusted
Location:
Boston, MA
Last seen:
1 day, 7 hours ago
Joined:
3 years, 4 months ago
Email:
l**********@gmail.com

Posts by Lina F

<prev • 76 results • page 1 of 8 • next >
0
votes
1
answer
112
views
1
answers
Comment: C: Visualizing whole genome alignment beyond dotplots
... 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 12 days ago by Lina F110
0
votes
1
answer
112
views
1
answers
Comment: C: Visualizing whole genome alignment beyond dotplots
... 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 12 days ago by Lina F110
0
votes
1
answer
112
views
1
answer
Visualizing whole genome alignment beyond dotplots
... 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 ...
dotplot alignment visualization whole genome written 12 days ago by Lina F110 • updated 12 days ago by h.mon11k
0
votes
1
answer
296
views
1
answers
Comment: C: Removing common SNPs from a set of VCF files
... Great, thanks for pointing me in the right direction! ...
written 4 months ago by Lina F110
3
votes
1
answer
296
views
1
answer
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 4 months ago by Lina F110
0
votes
0
answers
212
views
0
answers
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 4 months ago by Lina F110
0
votes
0
answers
212
views
0
answers
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 4 months ago by Lina F110
0
votes
0
answers
333
views
0
answers
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 5 months ago by Lina F110
1
vote
0
answers
333
views
0
answers
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 5 months ago by Lina F110
0
votes
1
answer
354
views
1
answers
Comment: C: Align two microbial genomes -- is mummer still the way to go?
... Great, thanks for the suggestion, I will take a look! ...
written 6 months ago by Lina F110

Latest awards to Lina F


Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 586 users visited in the last hour