Reference Code backup Executable files
This module is used to check the nucleotide composition bias. Due to random priming, certain patterns are over represented at the beginning (5’end) of reads. This bias could be easily examined by NVC (Nucleotide versus cycle) plot. NVC plot is generated by overlaying all reads together, then calculating nucleotide composition for each position of read (or each sequencing cycle). In ideal condition (genome is random and RNA-seq reads is randomly sampled from genome), we expect A%=C%=G%=T%=25% at each position of reads.
read_NVC.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o output
| --version | show program’s version number and exit |
| -h, --help | show this help message and exit |
| -i INPUT_FILE, --input-file=INPUT_FILE | |
| Input file in BAM or SAM format.[required] | |
| -o OUTPUT_PREFIX, --out-prefix=OUTPUT_PREFIX | |
| Prefix of output files(s). [required] | |
| -x, --nx | Flag option. Presense of this flag tells program to include N,X in output NVC plot [required] |
| -q MAP_QUAL, --mapq=MAP_QUAL | |
| Minimum mapping quality (phred scaled) for an alignment to be called “uniquely mapped”. default=30 | |