User: ikangkim

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ikangkim40
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6 months ago
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2 years, 8 months ago
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Posts by ikangkim

<prev • 9 results • page 1 of 1 • next >
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Comment: C: Illumina polishing after PacBio assembly and polishing?
... Thank you for a comment. I've never thought about 'hot spot' for indels. Nowadays, I'm checking the Pilon results more carefully, and sometimes run Pilon with "--fix bases" option to disallow large changes. Thanks. ...
written 6 months ago by ikangkim40
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Comment: C: Abnormal per sequence GC content and weird sequences in bacterial RNA-seq
... Thanks for your suggestion. Because I came to know that ~10% of reads at the stress condition were mapped onto rRNA genes (despite rRNA depletion), I performed taxonomic classification of randomly-sampled reads against Silva SSU rRNA database using classify.seqs command available in Mothur. The re ...
written 10 months ago by ikangkim40
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Abnormal per sequence GC content and weird sequences in bacterial RNA-seq
... Hi, I'm analyzing my first RNA-seq results that were obtained from a bacterial strain at two conditions: control vs. stress. Because the bowtie2 mapping ratio of stress condition was much lower (57%) compared to control (86%), I looked into the FastQC results and also manually checked sequences. ...
rna-seq sequencing written 10 months ago by ikangkim40
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Comment: C: Illumina polishing after PacBio assembly and polishing?
... Thank you for a comment. (1) I didn't know that PacBio has systematic deletion at homopolymer regions. (2) Below is the IGV snapshot image of the region where Pilon introduced 43 bp deletion. Upper is the PacBio read mapping, while the lower is the Illumina read mapping. All PacBio reads were mapp ...
written 12 months ago by ikangkim40
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Illumina polishing after PacBio assembly and polishing?
... Hi, If genome sequences were assembled from PacBio reads and then polished with quiver/arrow iteratively, do I steel need to polish the genome sequences further with Illumina reads? I've been trying to assemble a few dozen actinobacterial genomes. I have both PacBio and Illumina data and sequencin ...
genome assembly sequencing written 13 months ago by ikangkim40
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Comment: C: Are there advantages in using high accuracy models for guppy basecaller when Ill
... I've been trying to optimize several parameters for guppy. Until now, the setting below was the fastest for GPU, but the speed improvement was just ~20-25% compared to default. $ guppy_basecaller -i /fast5 -s /guppy -c dna_r9.4.1_450bps_hac.cfg -x "cuda:0" --gpu_runners_per_device 4 --num_callers ...
written 13 months ago by ikangkim40
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Comment: C: Are there advantages in using high accuracy models for guppy basecaller when Ill
... Thank you for a reply. I also feel that hac models would be better for downstream analyses. I think I had better spend more time to optimize guppy parameters. Currently, hac model is >10X (GPU) or >20X (CPU) slower than fast model on my machine. ...
written 13 months ago by ikangkim40
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Are there advantages in using high accuracy models for guppy basecaller when Illumina data are available?
... Hi, I'm planning to sequence bacterial genomes using both Nanopore and Illumina platforms to get nearly complete and accurate genomes. After getting sequence data, I'm going to perform hybrid assembly (e.g. Unicycler) or long-read assembly followed by short-read polishing. In this case, can I get ...
genome assembly sequencing written 13 months ago by ikangkim40
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Answer: A: SPAdes assembler k-mer > default 127 possible?
... https://github.com/ablab/spades/issues/40 The above page may be helpful for you. I tried with SPAdes 3.11.1 and succeeded. In brief, (1) To use k-mer > 127, you have to download and compile source code. (2) Edit "spades_compile.sh" file as below and run the script. cmake -G "Unix Makefiles" ...
written 2.7 years ago by ikangkim40

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Scholar 2.6 years ago, created an answer that has been accepted. For A: SPAdes assembler k-mer > default 127 possible?
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: SPAdes assembler k-mer > default 127 possible?

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