TEToolkit 2.0.3

Requirements

Python: 2.6.x or 2.7.x (not tested in Python 3.x)

pysam: 0.9.x or greater

R: 2.15.x or greater

DESeq2: 1.10.x or greater

Installation

1. Download compressed tarball.

2. Unpack tarball.

3. Navigate into unpacked directory.

4. Run the following:

   $ python setup.py install

If you want to install locally (e.g. /local/home/usr), run this command instead:

$ python setup.py install --prefix /local/home/usr

NOTE In the above example, you must add

/local/home/usr/bin

to the PATH variable, and

/local/home/usr/lib/python2.X/site-packages

to the PYTHONPATH variable, where python2.X refers to the python version (e.g. python2.7 if using python version 2.7.x).

Usage

usage: TEtranscripts -t treatment sample [treatment sample ...]
                     -c control sample [control sample ...]
                     --GTF genic-GTF-file
                     --TE TE-GTF-file
                     [optional arguments]

Required arguments:
  -t | --treatment [treatment sample 1 treatment sample 2...]
     Sample files in group 1 (e.g. treatment/mutant), separated by space
  -c | --control [control sample 1 control sample 2 ...]
     Sample files in group 2 (e.g. control/wildtype), separated by space
  --GTF genic-GTF-file  GTF file for gene annotations
  --TE TE-GTF-file      GTF file for transposable element annotations

Optional arguments:

  *Input/Output options*
  --format [input file format]
     Input file format: BAM or SAM. DEFAULT: BAM
  --stranded [option]   Is this a stranded library? (yes, no, or reverse).
                        DEFAULT: yes.
  --sortByPos           Input file is sorted by chromosome position.
  --project [name]      Prefix used for output files (e.g. project name)
                        DEFAULT: TEtranscript_out

  *Analysis options*
  --mode [TE counting mode]
     How to count TE:
        uniq        (unique mappers only)
        multi       (distribute among all alignments).
     DEFAULT: multi
  --minread [min_read] read count cutoff. DEFAULT: 1
  -L | --fragmentLength [fragLength]
     Average length of fragment used for single-end sequencing
     DEFAULT: For paired-end, estimated from the input alignment file. For single-end, ignored by default.
  -i | --iteration
     maximum number of iterations used to optimize multi-reads assignment. DEFAULT: 100
  -p | --padj [pvalue]
     FDR cutoff for significance. DEFAULT: 0.05
  -f | --foldchange [foldchange]
     Fold-change ratio (absolute) cutoff for differential expression.
     DEFAULT: 1

  *DESeq1 compatibility options*
  --DESeq
     Use DESeq (instead of DESeq2) for differential analysis.
  -n | --norm [normalization]
     Normalization method : DESeq_default (default normalization method of DESeq), TC (total annotated read counts), quant (quantile normalization). Only applicable if DESeq is used instead of DESeq2.
     DEFAULT: DESeq_default

  *Other options*
  -h | --help
     Show help message
  --verbose [number]
     Set verbose level.
       0: only show critical messages
       1: show additional warning messages
       2: show process information
       3: show debug messages
     DEFAULT: 2
  --version
     Show program's version and exit

NOTE BAM files must be either unsorted or sorted by queryname. If the BAM files are sorted by position, please use the ‘–sortByPos’ option

Example Command Lines

If BAM files are unsorted, or sorted by queryname:

TEtranscripts --format BAM --mode multi -t RNAseq1.bam RNAseq2.bam -c CtlRNAseq1.bam CtlRNAseq.bam --project sample_nosort_test

If BAM files are sorted by coordinates/position:

TEtranscripts --sortByPos --format BAM --mode multi -t RNAseq1.bam RNAseq2.bam -c CtlRNAseq1.bam CtlRNAseq.bam --project sample_sorted_test

Usage

usage: TEcount -b RNAseq BAM
               --GTF genic-GTF-file
               --TE TE-GTF-file
               [optional arguments]

Required arguments:
  -b | --BAM alignment-file  RNAseq alignment file (BAM preferred)
  --GTF genic-GTF-file       GTF file for gene annotations
  --TE TE-GTF-file           GTF file for transposable element annotations

Optional arguments:

  *Input/Output options*
  --format [input file format]
     Input file format: BAM or SAM. DEFAULT: BAM
  --stranded [option]   Is this a stranded library? (yes, no, or reverse).
                        DEFAULT: yes.
  --sortByPos           Input file is sorted by chromosome position.
  --project [name]      Prefix used for output files (e.g. project name)
                        DEFAULT: TEcount_out

  *Analysis options*
  --mode [TE counting mode]
     How to count TE:
        uniq        (unique mappers only)
        multi       (distribute among all alignments).
     DEFAULT: multi
  -L | --fragmentLength [fragLength]
     Average length of fragment used for single-end sequencing
     DEFAULT: For paired-end, estimated from the input alignment file. For single-end, ignored by default.
  -i | --iteration
     maximum number of iterations used to optimize multi-reads assignment. DEFAULT: 100

  *Other options*
  -h | --help
     Show help message
  --verbose [number]
     Set verbose level.
       0: only show critical messages
       1: show additional warning messages
       2: show process information
       3: show debug messages
     DEFAULT: 2
  --version
     Show program's version and exit

NOTE BAM files must be either unsorted or sorted by queryname. If the BAM files are sorted by position, please use the ‘–sortByPos’ option

Example Command Lines

If BAM files are unsorted, or sorted by queryname:

TEcount --format BAM --mode multi -b RNAseq.bam --project sample_nosort_test

If BAM files are sorted by coordinates/position:

TEtranscripts --sortByPos --format BAM --mode multi -b RNAseq.bam --project sample_sorted_test