User: nkuyfq

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nkuyfq60
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China
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1 week, 3 days ago
Joined:
5 years, 4 months ago
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n*****@163.com

Posts by nkuyfq

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Tools for downsampling/resampling/subsampling Oxford Nanopore reads
... @WouterDeCoster, due to some currently insoluble issues about the internet services, I am unable to use the ADD COMMENT or ADD REPLY to response to you. I will try to re-sample the MinION reads as you suggested. nkuyfq@163.com From: WouterDeCoster on Biostar Date: 2019-09-11 18:00 To: nkuyfq Sub ...
written 10 days ago by nkuyfq60
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Comment: A: Tools for downsampling/resampling/subsampling Oxford Nanopore reads
... I want to explore the lower threshold of the read number, like 1000, 1500 or 2000, which is sufficient to identify the target virus. Unlike next-generation sequencing platforms generating reads with uniform read length, MinION-generated reads might own some sort of distribution in read length. In ...
written 11 days ago by nkuyfq60
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Tools for downsampling/resampling/subsampling Oxford Nanopore reads
... I have got ~40000 MinION reads derived from a virus, whose read length ranges from ~100 to ~34.9k. I would like to re-sample these reads to evaluate the minimum read number enough to detect this virus. As Oxford nanopore reads have no identical read length, I have to take the varying read length int ...
nanopore written 11 days ago by nkuyfq60
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How to generate identity matrix files using Mauve?
... I am using Mauve to compare multiple genomes. On the mannual page http://asap.ahabs.wisc.edu/mauve-aligner/mauve-user-guide/mauve-output-file-formats.html, the author said an identity matrix file of the genomes compared could be generated. However, under command-line condition, I couldn't generate ...
genomics written 4.9 years ago by nkuyfq60 • updated 4.9 years ago by Biostar ♦♦ 20
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Comment: C: How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using QIIME?
... Hi, sheridan! I seemed to have found a solution. The mapping file (one for per sample) should be like this: #SampleID    BarcodeSequence    LinkerPrimerSequence   Description ID1        ACACTGACGACATGGTTCTACAGTGCCAGCMGCCGCGGTAA    ID1 You may find that the field corresponding to 'BarcodeSequence' ...
written 5.0 years ago by nkuyfq60
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Comment: C: How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using QIIME?
... I have barcode sequences for all samples. But I don't have the so-called barcode fastq files required by QIIME. The Miseq instrument has demultiplexed all samples for me, therefore there is no need to use the demultiplex function of QIIME at all. I only want to use quality control function of the ` ...
written 5.0 years ago by nkuyfq60
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Answer: A: How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using QIIME?
... I have barcode sequences for all samples. But I don't have the so-called barcode fastq files required by QIIME. The Miseq instrument has demultiplexed all samples for me, therefore there is no need to use the demultiplex function of QIIME at all. I only want to use quality control function of the ` ...
written 5.0 years ago by nkuyfq60
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How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using QIIME?
... I have sequenced several samples on Ilumina Miseq, generating paired-end reads (2*250bp) spanning V3-V4 region of 16S rDNA. I want to analyze these samples with QIIME v1.8. The script `split_libraries_fastq.py` in QIIME aimes to demultiplex and quality filter raw fastq seqeunces, with seperate fast ...
next-gen sequencing written 5.0 years ago by nkuyfq60 • updated 3.3 years ago by tovia0
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Comment: C: How to calculate organism relative abundance from Illumina metagenomic data?
... Thanks, I will have a try. ...
written 5.4 years ago by nkuyfq60
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Comment: C: How to calculate organism relative abundance from Illumina metagenomic data?
... Metaphlan seems only cover Bacteria and Archaea, which is a limiting factor for its use in Viral and Fungal metagenome. Kraken is likely to be a resource-intensive software, but it's quite fast. ...
written 5.4 years ago by nkuyfq60

Latest awards to nkuyfq

Great Question 4.9 years ago, created a question with more than 5,000 views. For How to calculate organism relative abundance from Illumina metagenomic data?
Great Question 4.9 years ago, created a question with more than 5,000 views. For How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using QIIME?
Epic Question 4.9 years ago, created a question with more than 10,000 views. For How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using QIIME?
Popular Question 4.9 years ago, created a question with more than 1,000 views. For How to generate identity matrix files using Mauve?
Popular Question 4.9 years ago, created a question with more than 1,000 views. For How to calculate organism relative abundance from Illumina metagenomic data?
Popular Question 4.9 years ago, created a question with more than 1,000 views. For How to deal with demultiplexed Miseq pair-end (2*250bp) 16S data using QIIME?

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