User: andorjkiss

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andorjkiss10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
1 month, 1 week ago
Joined:
5 years, 10 months ago
Email:
a*********@gmail.com

Posts by andorjkiss

<prev • 17 results • page 1 of 2 • next >
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Augustus Training | Multi-thread autoAug.pl?
... Is it possible to mutli-thread the autoAug.pl script for the Augustus training? If so, how would one do that? And, how long would training Augustus take for the *Xenopus tropicalis* (1.7 Gbp) genome (fully annotated by Genbank)? ...
genome assembly augustus training annotation written 5 weeks ago by andorjkiss10
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Comment: C: Guppy basecaller ONT
... Hi, If you set-up your NVIDIA drivers and CUDA toolkit properly, you just have to download the GUPPY for GPU tarball (64-bit) and then decompress the tarball, and execute the basecaller: ./ont-guppy/bin/guppy_basecaller -i input_dir -r -s output_dir/ -c dna_r9.4.1_450bps_hac.cfg -x 'cuda:0 cud ...
written 8 months ago by andorjkiss10
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Answer: A: best kmer for genome size estimation
... There are some good papers on exactly this topic: 1. https://arxiv.org/pdf/1308.2012.pdf 2. https://www.researchgate.net/publication/309590499_KAT_A_K-mer_Analysis_Toolkit_to_quality_control_NGS_datasets_and_genome_assemblies 3. https://kat.readthedocs.io/en/latest/walkthrough.html ...
written 9 months ago by andorjkiss10
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Comment: C: De novo pacBio genome assembly: How to polish data without quiver?
... The metrics on this programme look excellent and it's a separate step; after assembly. ...
written 9 months ago by andorjkiss10
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Comment: C: Pipeline for hybrid genome assembly of long and short reads AND how to deal with
... Hi, How long did the HGAP4 assembler take and what was the size of your genome? ...
written 10 months ago by andorjkiss10
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Comment: C: What is the appropriate assembler for PacBio long reads
... I'd stay away from PacBio based assemblers - they're pretty difficult to get to work and take FOREVER. Use a third party assembler, like CANU. ...
written 10 months ago by andorjkiss10
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Comment: C: What kind of Affymetrix SNP 6.0 datafile is this?
... Okay, I've found the CEL files, the CHP files and studied how to do this via Bioconductor in R. I think that the RMA has been done and might already be in the CHP file(s). However, in the event that I need to normalise myself, I would have to choose an appropriate database file for the normalizati ...
written 14 months ago by andorjkiss10
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Comment: C: What kind of Affymetrix SNP 6.0 datafile is this?
... Okay, thanks - this is very helpful. What we're ultimately trying to do is to use a programme called "InFlo" that makes use of datasets (RNA-Seq; WGS; WXS; SNP; Methylation) to build network maps. So, their input example file (https://github.com/VaradanLab/InFlo) is apparently L3 RMA Normalised (h ...
written 14 months ago by andorjkiss10
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Comment: C: What kind of Affymetrix SNP 6.0 datafile is this?
... Sure, it's from the Osteosarcoma public data set at TARGET: https://ocg.cancer.gov/programs/target/data-matrix ...
written 14 months ago by andorjkiss10
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Comment: A: What kind of Affymetrix SNP 6.0 datafile is this?
... So this is un-normalised data, correct? And if I wanted normalised data (say L3 RMA-normalised) I would have to obtain the CEL/CDF files? Am I correct about this for normalisation? TIA ...
written 14 months ago by andorjkiss10

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Popular Question 8 months ago, created a question with more than 1,000 views. For Total RNA Commercial Kit Comparison Study
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Total RNA Commercial Kit Comparison Study

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