### Example data for testing installation of TEtranscripts ###

To test whether your installation of the TEtranscripts is working properly, we have provided sample files for a test run.

### TEtranscripts ###
## Using version 2.0.5

# Single-end (testdata_SE folder)

Input files: testData_treatment_rep1_SE.bam testData_treatment_rep2_SE.bam testData_control_rep1_SE.bam testData_control_rep2_SE.bam
GTF files (testdata_GTF folder): dm3_refGene.gtf, dm3_rmsk_TE.gtf
   # You will need to decompress them before use.
CMD line:
   TEtranscripts --sortByPos --mode multi --TE dm3_rmsk_TE.gtf --GTF dm3_refGene.gtf --project singleEnd_test -t testData_treatment_rep1_SE.bam testData_treatment_rep2_SE.bam -c testData_control_rep1_SE.bam testData_control_rep2_SE.bam 2>log

The expected output files are:
  singleEnd_test.cntTable
  singleEnd_test_DESeq2.R
  singleEnd_test_gene_TE_analysis.txt
  singleEnd_test_sigdiff_gene_TE.txt

# Paired-end (testdata_PE folder)

Input files: testData_treatment_rep1_PE.bam testData_treatment_rep2_PE.bam testData_control_rep1_PE.bam testData_control_rep2_PE.bam
GTF files (testdata_GTF folder): hg19_refGene.gtf, hg19_rmsk_TE.gtf
   # You will need to decompress them before use.
CMD line:
   TEtranscripts --sortByPos --mode multi --TE hg19_rmsk_TE.gtf --GTF hg19_refGene.gtf --project pairedEnd_test -t testData_treatment_rep1_PE.bam testData_treatment_rep2_PE.bam -c testData_control_rep1_PE.bam testData_control_rep2_PE.bam 2> log

The expected output files are:
  pairedEnd_test.cntTable
  pairedEnd_test_DESeq2.R
  pairedEnd_test_gene_TE_analysis.txt
  pairedEnd_test_sigdiff_gene_TE.txt


### TECount ###
## using version 2.0.5

# Single-end (testdata_SE folder)

Input files: testData_treatment_rep1_SE.bam 
GTF files (testdata_GTF folder): dm3_refGene.gtf, dm3_rmsk_TE.gtf
   # You will need to decompress them before use.
CMD line:
   TEcount --sortByPos --mode multi --TE dm3_rmsk_TE.gtf --GTF dm3_refGene.gtf --project treatment_rep1_SEtest -b testData_treatment_rep1_SE.bam 2>log

The expected output file is:
  treatment_rep1_SEtest.cntTable

# Paired-end (testdata_PE folder)

Input files: testData_treatment_rep1_PE.bam
GTF files (testdata_GTF folder): hg19_refGene.gtf, hg19_rmsk_TE.gtf
   # You will need to decompress them before use.
CMD line:
   TEcount --sortByPos --mode multi --TE hg19_rmsk_TE.gtf --GTF hg19_refGene.gtf --project treatment_rep1_PEtest -b testData_treatment_rep1_PE.bam 2>log

The expected output file is:
  treatment_rep1_PEtest.cntTable