Recent Changes

Tuesday, March 19

  1. page Unix Commands edited ... /home cp: copy files cp dir1/foo.txt /dir2/ dir2/ ## copies foo.txt from dir1 to dir2 c…
    ...
    /home
    cp: copy files
    cp dir1/foo.txt /dir2/dir2/
    ## copies foo.txt from dir1 to dir2
    cp -r dir1/dir2/dir1/ dir2/
    ## copies dir1 and its contents to dir2
    ls: list the contents in a directory
    (view changes)
    7:18 am
  2. page Unix Commands edited ... /home cp: copy files cp /dir1/foo.txt dir1/foo.txt /dir2/ ## copies foo.txt from dir1 to…
    ...
    /home
    cp: copy files
    cp /dir1/foo.txtdir1/foo.txt /dir2/
    ## copies foo.txt from dir1 to dir2
    cp -r /dir1/ /dir2/dir1/dir2/
    ## copies dir1 and its contents to dir2
    ls: list the contents in a directory
    (view changes)
    7:17 am

Friday, February 1

  1. page Scripts edited Bellow is a collection of various scripts and tools that have been useful for analyzing next-gen da…
    Bellow is a collection of various scripts and tools that have been useful for analyzing next-gen data. Some of the scripts have been written for personal use and may be buggy or unintuitive. However, they are all free and can usually be coaxed into working or can serve as springboards for accomplishing other tasks. Many of the python scripts require the screed library which can be downloaded here.
    Navigate to:
    General Raw Read Scripts"
    General Statistics for manipulating raw reads:
    Download the file in scripts --- I will update this with location of these scripts on the bigmac.
    http://sfg.stanford.edu/

    Read statistics
    Fastqc: A quality control tool for high throughput sequence data.
    Quality trimming
    q-trim.py:q-trim.py {q-trim.py} : Trims sequences
    both.py: Extracts only reads that have both R1 and R2 sequences. Input 2 files, one with the R1 and another with the R2 reads. Can be useful after quality trimming to make sure you only use sequences for which both reads exist in down stream applications. Written to work with data generated using Illumina's pipeline CASAVA 1.8 and higher.
    Shuffle and subset paired end sequences
    (view changes)
    9:21 am

Monday, August 6

  1. 7:40 am

Friday, June 22

  1. page Home edited ... The basics of working remotely Working on Remote Machines Queuing Systems - TO UPDATE Com…
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    The basics of working remotely
    Working on Remote Machines
    Queuing Systems - TO UPDATE
    Computing Resources on Campus
    Tutorials
    (view changes)
    2:09 pm
  2. page Ques (deleted) edited
    2:09 pm
  3. 2:09 pm

Monday, June 18

  1. page DESeq edited ... use <- (rs > 10) countTableFilt <- countTable[ use, ] ... adult. In this the c…
    ...
    use <- (rs > 10)
    countTableFilt <- countTable[ use, ]
    ...
    adult. In thisthe case where
    #replicates
    conds <- factor( c( "larva", "larva", "adult", "adult" ) )
    ...
    "The inference in DESeq relies on an estimation of the typical relationship between the data’s variance and their mean, or, equivalently, between the data’s dispersion and their mean. The dispersion can be understood as the square of the coefficient of biological variation. So, if a gene’s expression typically differs from replicate to replicate sample by 20%, this gene’s dispersion is 0.22 = .04... Without any replicates at all, the estimateDispersions function will refuse to proceed unless we instruct it to ignore the condition labels and estimate the variance by treating all samples as if they were replicates of the same condition."
    #With biological replicates or with partial replicates.
    #In the case with#When you have partial replicates
    cds <- estimateDispersions( cds )
    #without biological replicates
    (view changes)
    8:51 am

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