User: xb

gravatar for xb
xb400
Reputation:
400
Status:
Trusted
Location:
Chapel Hill, NC,USA
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Google Scholar Page
Last seen:
3 years ago
Joined:
7 years, 2 months ago
Email:
x***************@gmail.com

Posts by xb

<prev • 30 results • page 1 of 3 • next >
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Answer: A: About gene expression heatmap
... R heatmap.2 or Java TreeView ...
written 4.9 years ago by xb400
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Answer: A: Can bowtie2-build index for gzipped file?
... It seems bowtie2-build won't work with pipeline by "|", though bowtie2 does. (Bowtie 2 version 2.2.3) Try the command below? It works with small .fa.gz files; haven't tested with large files yet ! bowtie2-build -c $(zcat filename.fa.gz | awk '/^>/&&NR>1{printf ","}{ printf "%s",/^> ...
written 4.9 years ago by xb400
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Comment: C: Differnces between PWM derived from SELEX and ChIP-seq
... Yes, if you have the matrix only. ...
written 4.9 years ago by xb400
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Answer: A: Differnces between PWM derived from SELEX and ChIP-seq
... The TFBSs by ChIP-seq data are usually divided into different groups (strong and weak, sometimes with an intermediate group: moderate) based on their binding strength. A common assumption is that "ChIP-seq signal values are correlated with the affinity of the TF-DNA binding" [ * ] PWM alone helps u ...
written 4.9 years ago by xb400
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Answer: A: Convert Phred score 41 to 40
... Is this what you want? cat <your-fastq-file> | awk ' {if(NR %4 == 0) {gsub("J","I");print} else {print}}' If it is a .gz file, use zcat to read it and gzip to zip it back.   ...
written 4.9 years ago by xb400
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Comment: C: Linux command line use to rename a gff annotation file "Name" attribute
... I tested your command and it works well. One thing to make sure is that the file field delimiter is "\t"instead of space. ...
written 4.9 years ago by xb400
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Answer: A: How do experienced people look for full reference genomes?
... You can first go with either ncbi or ensembl Escherichia coli (*.faa files in subfolders) ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/ Saccharomyces cerevisiae ftp://ftp.ensembl.org/pub/release-75/fasta/saccharomyces_cerevisiae/dna/   ...
written 4.9 years ago by xb400
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Comment: C: Linux command line use to rename a gff annotation file "Name" attribute
... @rob234king You are very welcome! Try this to keep "_M",  cat <your-file> | awk 'BEGIN{FS="\t";OFS="\t"} {if (gsub(/Name=[0-9]+_M;/,$9)==1) {print} else {s=gensub(/([[:alpha:]]*=)[^[:digit:];]*([[:digit:]]+)[^[:digit:];]*(;.+)/,"\\1\\2\\3\\4", "g", $9); print $1,$2,$3,$4,$5,$6,$7,$8,s} }'   ...
written 4.9 years ago by xb400
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Answer: A: Linux command line use to rename a gff annotation file "Name" attribute
... One of possible solutions ## 1) only cat <your-file> | awk 'BEGIN{FS="\t";OFS="\t"} {s=gensub(/([[:alpha:]]*=)[^[:digit:];]*([[:digit:]]+)[^[:digit:];]*(;.+)/,"\\1\\2\\3", "g", $9); print $1,$2,$3,$4,$5,$6,$7,$8,s}' ## output Chromosome_2_Copy       maker   gene    60155   61282   .       ...
written 4.9 years ago by xb400
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Answer: A: Tissue specific gene and housekeeping gene
... Will this give you any hints ? - if the species in your study is Human Identification of Human HK Genes and Gene Expression Regulation Study in Cancer from Transcriptomics Data Analysis To get the first introns, please refer to these topics in the forum, Question: How To Find Intron Sequences Fro ...
written 4.9 years ago by xb400

Latest awards to xb

Teacher 4.3 years ago, created an answer with at least 3 up-votes. For A: Linux command line use to rename a gff annotation file "Name" attribute
Scholar 4.9 years ago, created an answer that has been accepted. For A: Linux command line use to rename a gff annotation file "Name" attribute
Scholar 4.9 years ago, created an answer that has been accepted. For A: Linux command line use to rename a gff annotation file "Name" attribute
Appreciated 4.9 years ago, created a post with more than 5 votes. For A: Question About Hellinger Distances And Principle Coordinates Analysis
Scholar 4.9 years ago, created an answer that has been accepted. For A: Linux command line use to rename a gff annotation file "Name" attribute
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Question About Hellinger Distances And Principle Coordinates Analysis
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: Changing File Names In R
Appreciated 5.4 years ago, created a post with more than 5 votes. For A: Question About Hellinger Distances And Principle Coordinates Analysis
Teacher 5.4 years ago, created an answer with at least 3 up-votes. For A: Question About Hellinger Distances And Principle Coordinates Analysis

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