To do a project recently, I need to use the RNA-SeQC.jar package to analyze the gene sequencing results.
1. Parameter input
-n 1000 -s \"TestId|ThousandReads.bam|TestDesc\" -t gencode.v7.annotation_goodContig.gtf -r Homo_sapiens_assembly19.fasta -o ./testReport/ -strat gc -gc gencode.v7.gc.txt
2. Document preparation
ThousandReads.bam must be indexed, and use BuildBamIndex to generate a file with the same name ending in bai.
3. Parameter verification
Input parameter option initialization.
Options opts = setupCliOptions();、
-s Sample File (text-delimited description of samples and their bams)(必须)
-t GTF File defining transcripts (must end in '.gtf').(必须)
-r Reference Genome in fasta format. (必须)
-o Output directory (will be created if doesn't exist).(必须)
-n Number of top transcripts to use. (not required)
-d Perform downsampling to the given number of reads.(非必须)
-e Change the definition of a transcripts end (5' or 3') to the given length. (10, 50, 100 are acceptable values)(非必须)
-rRNA intervalFIle for rRNA loci (must end in .list) (optional)
-corr GCT file for expression correlation comparison (not required)
-gc File of transcript id <tab> gc content. Used for stratification.(非必须)
-strat Stratification options: current supported option is 'gc' (非必须)
-expr Uses provided GCT file for expression values instead of on-the-fly RPKM calculation(非必须)
-BWArRNA Use an on the fly BWA alignment for estimating rRNA content. The value should be the rRNA reference fasta. (非必须)
-ttype The column in gtf to use to look for rRNA transcript type(非必须)
-bwa Path to BWA, which should be set if it's not in your path and BWArRNA is used.(非必须)
-rRNAdSampleTarget Downsamples to calculate rRNA rate more efficiently. Default is 1 million. Set to 0 to disable.(非必须)
-gcMargin Used in conjunction with '-strat gc' to specify the percent gc content to use as boundaries. E.g. .25 would set a lower cutoff of 25% and an upper cutoff of 75%.(非必须)
-gatkFlags A string of flags that will be passed on to the GATK (非必须)
Check parameters
code show as below:
checkArgs (cl) ；
The main check -e option must be one of three numbers Acceptable values for e are 50, 100 or 200
-t must be a gtf file