User: Louis Kok

gravatar for Louis Kok
Louis Kok10
Reputation:
10
Status:
New User
Location:
Singapore
Last seen:
2 days, 17 hours ago
Joined:
4 years, 3 months ago
Email:
e*********@gmail.com

Posts by Louis Kok

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Column explanation for repeat database from UCSC
... Hi @RamRS. Added a few lines. ...
written 5 weeks ago by Louis Kok10
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Column explanation for repeat database from UCSC
... I was looking into the repeat database from UCSC as below: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/rmsk.txt.gz This file does not contain a header. Can I check what those columns are so that I can better understanding the meaning? Thanks in advance. A few lines of the file is a ...
repeats rmsk ucsc written 5 weeks ago by Louis Kok10 • updated 5 weeks ago by finswimmer12k
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Samtools mpileup - Sudden decrease of coverage at homopolymer regions
... When generating output of samtools mpileup, I notice there is sudden decrease of coverage at the homopolymer region and went up again at position 250 to 261. I have check with IGV and confirmed that there is no gap /insertion happening around the region. My command is as below: samtools mpileup ...
samtools mapping mpileup written 3 months ago by Louis Kok10 • updated 3 months ago by Kevin Blighe46k
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Extracting the coordinates for a specific base from multifasta
... Hi, I would like to extract coordinates for a specific base, let say all "A" base from multi-fasta. The way I I used to extract from a single sequence (without header) is as below: grep -aob "A" input.seq | sed 's/:/ /g' | awk '{print $1+1}' Is there an easier way to deal with large and mult ...
fasta sequence written 8 months ago by Louis Kok10 • updated 8 months ago by jrj.healey13k
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Possible reason for no peaks generated by MACS2
... Hi, I am new to ChIP-Seq data analysis. In my samples, the expression of transcription factor of interest was observed to be down-regulated. Subsequently, a ChIP-Seq on this transcription factor of interest in three replicates was performed and input DNA was used as control. Initially when I perform ...
macs chip-seq written 10 months ago by Louis Kok10 • updated 9 months ago by Biostar ♦♦ 20
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Comment: C: Viewing the sai file generated using bwa
... Yes. I have the fastq but do not know what the reference it was mapped to. ...
written 13 months ago by Louis Kok10
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Viewing the sai file generated using bwa
... Hi. I am working on RNA-Seq analysis which was partially done by a researcher who left the team. The only mapping files that I have is the sai files but not the bam files. May I know if there is a way to view the content of the sai files? Thanks in advance. ...
mapping bwa written 13 months ago by Louis Kok10 • updated 13 months ago by noahaus10
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Hierarchical ranking of gene ontology
... Hi all. I have a question about the gene ontology ranking. For example, GO:0004672 is named as protein kinase activity. From the Tree view, I found that it can be linked to different higher level, such as macromolecule modification, protein metabolic process and others at level 5. I would like class ...
gene ontology written 3.2 years ago by Louis Kok10
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Comment: C: 16S rRNA database for human clinical pathogens?
... Dear Natasha, Many thanks for the information. This is certainly helpful. :) Rgds, Louis ...
written 3.4 years ago by Louis Kok10
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16S rRNA database for human clinical pathogens?
... Hi All, I was wondering if there is any available public 16S rRNA database specific for human bacterial pathogens, other than the generic databases like RDP or SILVA? Thank you. ...
16s pathogens database human written 3.4 years ago by Louis Kok10 • updated 3.4 years ago by natasha.sernova3.5k

Latest awards to Louis Kok

Popular Question 20 days ago, created a question with more than 1,000 views. For Hierarchical ranking of gene ontology
Great Question 8 months ago, created a question with more than 5,000 views. For Multiple asterisks inside amino acid fasta sequences
Popular Question 10 months ago, created a question with more than 1,000 views. For Hierarchical ranking of gene ontology
Popular Question 11 months ago, created a question with more than 1,000 views. For Hierarchical ranking of gene ontology
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Hierarchical ranking of gene ontology
Popular Question 3.0 years ago, created a question with more than 1,000 views. For TargetP Error: zero output generated
Popular Question 3.0 years ago, created a question with more than 1,000 views. For BLAST result is different between Sanger forward and reverse reads
Popular Question 3.0 years ago, created a question with more than 1,000 views. For How to interpret the outputs generated from bamtobed using BedTools?
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Obtain heterozyous/IUPAC consensus sequences from multiple sequence alignment
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Convert alignment in Fasta/Clustal format to SAM/BAM file
Popular Question 3.0 years ago, created a question with more than 1,000 views. For 16S rRNA database for human clinical pathogens?
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Convert alignment in Fasta/Clustal format to SAM/BAM file
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Convert alignment in Fasta/Clustal format to SAM/BAM file

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