User: Sus

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Sus20
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2 months ago
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1 year, 6 months ago
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Posts by Sus

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How does VFDB work?
... I will add that you can have a global look of their analysis pipeline in their paper: [https://www.ncbi.nlm.nih.gov/pubmed/30395255][1] Maybe with that information and the data you can get from their download page you can get somewhere. You can for instance, run a simple blast for the VF sequences ...
written 9 weeks ago by Sus20
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Comment: C: extract lines with multiple conditions on multiple fields/column
... Grouping the conditions and adding the "or" operator `||` should do the trick `awk -F "," '($3 >= 0.5 && $3 <= 1) || ($4 >= 0.5 && $4 <= 1) || ($5 >= 0.5 && $5 <= 1)' input.csv > out.csv` ...
written 10 weeks ago by Sus20
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Comment: C: Does Illumina Undetermined Fastq files contain barcodes
... The path for the file is `/Data/Intensities/BaseCalls/Alignment/` and is called `DemultiplexSummaryF1L1.txt` (I know the post is 18 month old but it could help someone in the future) ...
written 7 months ago by Sus20
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Comment: C: Difficulty retrieving NCBI taxonomic IDs from multiple accession IDs
... Alternatively if you cannot find your IDs you can look into the files prefixed `dead_` that keep a trace of old ids that either don't exists anymore or have been changed. I had to do something similar a few months ago and I found almost all acc IDs in the files listed here [https://ftp.ncbi.nlm.nih ...
written 7 months ago by Sus20
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Comment: C: 16S rRNA classification pipeline
... Right now I have illumina data targeting V3 & V4 ...
written 10 months ago by Sus20
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16S rRNA classification pipeline
... Hello everyone, I have 16S data and I'm trying to identify what genus/species etc. are in my samples and their relative abundance. It's my first time working with 16S data and I'm also not used to classification, I'm trying to improve what I already did and understand some concepts. As of today, ...
16s classifcation rna-seq written 10 months ago by Sus20 • updated 10 months ago by Kevin630
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Comment: C: Need Bioinformatics Help - Analyzing Unknown Dna Sequence
... Just a quick tip for using `omictools.com`, if you land on the annoying "subscribe for free" page, just use private navigation. ...
written 12 months ago by Sus20
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Trying to get consensus sequence from paired end alignment
... Hello ! I am trying to get a consensus sequence from my BAM file. For the context, I'm working with paired-end reads in fastq format, so far I've done: * Building the BWA index for my reference genome * Alignin with the BWA mem following this command: `bwa mem -t 16 ref.fa R1_1.fq R1_2.fq > al ...
paired-end alignment samtools bwa written 18 months ago by Sus20
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Some explanation about what a paired-end sequencing really means
... Hi ! I'm currently a student and I have a hard time understanding some basics of bioinformatics; I'm currently learning about *alignment*, *filtering*, *variant calling* and such so my question might look silly but here it is anyway. I have some trouble about how you work with paired-end sequencing ...
paired-end alignment written 18 months ago by Sus20 • updated 18 months ago by andrew.j.skelton735.8k

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Great Question 5 months ago, created a question with more than 5,000 views. For Some explanation about what a paired-end sequencing really means
Popular Question 12 months ago, created a question with more than 1,000 views. For Some explanation about what a paired-end sequencing really means

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