User: Lina F

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Lina F110
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110
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Location:
Boston, MA
Last seen:
1 day, 23 hours ago
Joined:
2 years, 12 months ago
Email:
l**********@gmail.com

Posts by Lina F

<prev • 71 results • page 1 of 8 • next >
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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 12 days 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 12 days 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 28 days 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 29 days 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 8 weeks 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 8 weeks 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 8 weeks 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 8 weeks ago by Lina F110
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Comment: C: Duplicates on Illumina
... I used the following code: seqtk mergepe R1.fastq.gz R2.fastq.gz > merged.fastq cat merged.fastq | awk -F'[: ]' '/@NB5/ {x=$6; y=$7; read=$8; line=NR} {if (NR==line+1 && read == 1){print $1, x, y}}' > reads_positions.txt sort reads_positions.txt > reads_positions_sorted ...
written 8 weeks ago by Lina F110
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Comment: C: Duplicates on Illumina
... Has this been resolved, and if yes, how? I checked some of our recent NextSeq runs and it seems to not be a problem. Thanks!! ...
written 9 weeks ago by Lina F110

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