Linux

Linux find examples

I just wanted to record a few short find commands that are very fast and useful. To find all the files modified on a specific date, in the case below the 13th May 2014: $ find . -type f -name "*" -newermt 2014-05-13 ! -newermt 2014-05-14 ./Phd/NI_genetic_data/SNPloci_update_May-2013/bed/male_Y_SNPS.hh ./Phd/NI_genetic_data/SNPloci_update_May-2013/bed/male_Y_SNPS.log ./Phd/NI_genetic_data/SNPloci_update_May-2013/bed/male_Y_SNPS.map ./Phd/NI_genetic_data/SNPloci_update_May-2013/bed/male_Y_SNPS.nof ./Phd/NI_genetic_data/SNPloci_update_May-2013/bed/male_Y_SNPS.ped ./Phd/NI_genetic_data/SNPloci_update_May-2013/bed/plink.hh ./Phd/NI_genetic_data/SNPloci_update_May-2013/bed/plink.log ./Phd/NI_genetic_data/SNPloci_update_May-2013/bed/plink.nof ./Presentations/Genemappers_2014/conference_notes/example_expression_variance.png ./Presentations/Genemappers_2014/conference_notes/notes_20140513.txt You can also append ls to the above to get more detailed information about the files:

Creating a QuasR target file using the terminal

I’ve just recieved some sequencing data from a couple of Illumina HiSeq lanes and need to run some QC and initial analyses for the miR RNA-seq experiment. As this my introduction into RNA-seq I’ve been doing a little reading and came across a very nice overview of using R/Bioconductor for RNA-seq analysis: Thomas Girke - Analysis of RNA-Seq Data with R/Bioconductor I’ve decided to give QuasR a go, I’ll report back either here or on the blog with progress.

Useful Linux sort variants

I just wanted a quick reference to look back on. You have a list of chromosomes in a random order: $ cat chr.list chr3 chr6 chr2 chr11 chr5 chr7 chr9 chr10 chr1 chr4 chr8 chr12 chr20 chr22 Default sort: $ cat chr.list | sort chr1 chr10 chr11 chr12 chr2 chr20 chr22 chr3 chr4 chr5 chr6 chr7 chr8 chr9 Sort with –version-sort: $ cat chr.list | sort --version-sort chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr20 chr22 Another way to get the same as above: