Comment on "Next generation sequencing in R or bioconductor environment"
R package SPP for chip-seq analysis. It can read quite a few aligner's output file. Here is the original package tutorial. http://compbio.med.harvard.edu/Supplements/ChIP-seq/tutoria...3637 days ago
Comment on "Encode sequencing data freely available to download and use for academic means"
The annotation file is available at http://www.nimblegen.com/downloads/annotation/hg19/3696 days ago
Comment on "Check the Size of a directory & Free disk space."
stat is also a nice command to know the detail statistics of the file. stat <fileName>3713 days ago
Comment on "Most Commonly used Awk by Bioinformatician"
Print line of a tab-delimited file when the 8th field is 10090:awk -F "\t" '$8 == 10090 { print $0 }' myFilePrint fields 1, 2, 3 from a tab-delimited file where the 4th field contains a '99':awk -F "\t" '$4 ~ /99/ {print $1"\t"$2"\t"$3}' myFile3724 days ago
Comment on "Bio++ : C Language libraries for your biological need"
...tral sequences).bppConsense (Build consensus trees and compute bootstrap values).bppSeqMan (Sequence manipulation and file format conversion).bppPhySamp (Sample sequences from a file according to a phylogenetic t...3840 days ago
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Comment on "Most Commonly used Awk by Bioinformatician"
To double space a file; $ awk '1; { print "" }' : To prints the number of words in a file; $ awk '{ total = total + NF }; END { print total+0 }' :3916 days ago
Comment on "Bio++ : C Language libraries for your biological need"
Parse FASTA/FASTQ file with C http://lh3lh3.users.sourceforge.net/parsefastq.shtml3927 days ago