Analyze gene expression based on coverage distribution around TSS from cfDNA
Basic Usage: expression_prediction.py [-h] -fq FASTQ_FILE -s NAME -g {m,f} [-o OUTDIR] [-k] [-t THREADS] -cna CNA_FILE [-tmp TEMP_DIR] [-step START_STEP]
Note: This calls every step of the below list. Copy number alterations (CNAs) need to be normalized against. This is done by specifying a list of copy-number states in the format . For plasma-seq analyses this is the *.segments file.
Attention: Large hg19 reference index files for BWA are not in this commit
Also needed for analysis: . java . R (Package e1071)
-) Step1 create directory and create MD5 file of input -) Step2 Trim fastq -) Step3 alignment and conversion to BAM -) Step4 remove PCR duplicates -) Step5 analyze TSS profile in housekeeping vs. unexpressed genes and plot in R -) Step6 extract coverage parameters for expression prediction -) Step7 expression prediction