Table 2 Comparison of functions and features of different QC tools for RNA-Seq data
From: RNA-QC-chain: comprehensive and fast quality control for RNA-Seq data
| Â | RNA-QC-Chain | RSeQC | RNA-SeQC |
|---|---|---|---|
Functions | |||
Quality evaluation of raw reads | Yes | Yes | No |
Quality trimming of raw reads | Yes | No | No |
rRNA detection | Yes | Yes | Yes |
rRNA removal | Yes | No | No |
Contaminating species identification | Yes | No | No |
Alignment statistics | Yes | Yes | Yes |
Features | |||
Language | C++ | Python and C | Java |
Input file (except commonly required files) | None | A chromosome size file and a BED file | An indexed bam file, a reference sequence, the index of reference sequence and a sequence dictionary |
Output format | FASTQ/FASTA, TXT, PNG, HTML | PDF, TXT | HTML |
Usage | One command line for each step | Multiple separate scripts | One command line |
rRNA reference file | A built-in rRNA database | Requires user to provide | Requires user to provide |
Visualization dependence | Gnuplot | UCSC Genome Browser or R scripts | N/A |
Parallel computation | Yes | No | No |
Running time for Dataset 1 (min) | 8 | 55 | 120 |