User: Nick

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Nick270
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Posts by Nick

<prev • 80 results • page 1 of 8 • next >
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Best Practice For Denovo Assembly of Bacterial Plasmids
... We are planning to sequence a few bacterial isolates. We decided to go for PacBio and aim at getting a large insert library (20k) as the genome of the species is known for extensive presence of repeats. We hope to get in this way contiguous assemblies for the chromosome. We worry about the plasmid ...
plasmid bacteria denovo written 3.4 years ago by Nick270
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Using qiime (or mothur) with 16S V1-V3 data
... I have Illumina PE reads of 16S V1-V3 data. I've already merged the reads and would like to analyse it using Qiime (or mothur). I assume the standard workflows have to be adapted as they rely on 16S V4 databases. Can anyone suggest a workflow which is specifically adjusted for V1-V3 data? ...
mothur 16s qiime written 3.4 years ago by Nick270 • updated 3.4 years ago by Istvan Albert ♦♦ 85k
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Comment: C: How To Annotate A Newly Sequenced Genome
... Prokka has trouble working with Spades. I'm getting "contig ID too long". Various blog posts suggests using some additional flags (e.g. --compliant, --centre) but so far I was not able to solve the issue. I know some have regressed to older versions of Prokka as the bug was introduced relatively rec ...
written 4.4 years ago by Nick270
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Downloading the raw 16S amplicon data for all saliva samples from the Human Microbiome Project
... I want to download the raw 16S amplicon data for all saliva samples from the Human Microbiome Project. However, I find the user interface somewhat confusing. Can someone advise how to proceed? ...
microbiome 16s hmp written 4.6 years ago by Nick270
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Comment: C: A pipeline for comparative bacterial genomics? Is it similar to comparative canc
... Thanks, dago. I've edited my question to make it more precise. Can you, perhaps, suggest a pipeline that would help me address this task? ...
written 4.7 years ago by Nick270
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Comment: C: A pipeline for comparative bacterial genomics? Is it similar to comparative canc
... Thanks, Dan. I've edited my question to make it more precise. Can you, perhaps, suggest a pipeline that would help me address this task? ...
written 4.7 years ago by Nick270
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A pipeline for comparative bacterial genomics involving cohorts (i.e. between group comparisons)?
... ==This is the original version of the question. Please jump to the edit below as it makes the question clearer. I don't have a lot of experience with bacterial NGS but have recently started working on a project that explores the differences (e.g. SNPs, indels) between bacterial strains. My first id ...
next-gen alignment snp written 4.7 years ago by Nick270
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Comment: C: What's wrong with this sample? (kmers found by FastQC of RNA-Seq)
... Thanks for suggesting to use the latest FastQC. The adaptor content is green (no issues identified). ...
written 4.7 years ago by Nick270
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What's wrong with this sample? (kmers found by FastQC of RNA-Seq)
... I've run FastQC on a sample of Illumina RNA-Seq. It identifies issues with abnormal kmer counts:   There is the as well the kmer table: What's wrong with this sample? What do I need to do? I reckon this points to a contamination of sorts. I've already run trimmomatic on this sample using the ...
rna-seq written 4.7 years ago by Nick270
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Are these samples de-multiplexed?
... I haven't done Illumina de-multiplxing before as the lab I am used to work with has done this by default. I'm now getting samples from a lab that says that it doesn't do de-multiplexing. It's a new lab which doesn't have experience with NGS so I am not quite sure they now what they are doing. So I g ...
illumina de-multiplxing miseq written 4.9 years ago by Nick270 • updated 4.9 years ago by Devon Ryan97k

Latest awards to Nick

Great Question 3.3 years ago, created a question with more than 5,000 views. For Trouble Installing Htseq-Count
Great Question 4.4 years ago, created a question with more than 5,000 views. For Easiest way to compute RNA-Seq mapping stats (exons, introns, intergenic)?
Great Question 4.4 years ago, created a question with more than 5,000 views. For The Easiest/Fastest Way To Get From Bam To Tpm Or Rpkm
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Large Number Of Macs Negative Peaks
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Why Does The Order Of -S And -M Parameters In Bowtie Matter?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Trouble Installing Htseq-Count
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Easiest way to compute RNA-Seq mapping stats (exons, introns, intergenic)?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Differential Expression Using Different Libraries (Truseq, Nextera)?
Popular Question 4.4 years ago, created a question with more than 1,000 views. For Trouble Installing Htseq-Count
Popular Question 4.7 years ago, created a question with more than 1,000 views. For Trouble Installing Htseq-Count
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Trouble Installing Htseq-Count
Popular Question 5.0 years ago, created a question with more than 1,000 views. For The Easiest/Fastest Way To Get From Bam To Tpm Or Rpkm
Popular Question 5.0 years ago, created a question with more than 1,000 views. For Differential Expression Using Different Libraries (Truseq, Nextera)?
Popular Question 5.1 years ago, created a question with more than 1,000 views. For Trouble Installing Htseq-Count
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Trouble Installing Htseq-Count
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Differential Expression Using Different Libraries (Truseq, Nextera)?
Popular Question 5.6 years ago, created a question with more than 1,000 views. For Differential Expression Using Different Libraries (Truseq, Nextera)?
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Trouble Installing Htseq-Count
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Weird Tophat2 Error Message
Popular Question 6.4 years ago, created a question with more than 1,000 views. For The Easiest/Fastest Way To Get From Bam To Tpm Or Rpkm
Popular Question 6.4 years ago, created a question with more than 1,000 views. For Replicates In Chip-Seq

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