| RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. |
hg clone https://toolshed.g2.bx.psu.edu/repos/nilesh/rseqc
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| estimates clipping profile of RNA-seq reads from BAM or SAM file | 5.0.1+galaxy2 | 20.01 | |
| calculates the fragment size for each gene/transcript | 5.0.1+galaxy2 | 20.01 | |
| calculate the inner distance (or insert size) between two paired RNA reads | 5.0.1+galaxy2 | 20.01 | |
| read coverage over gene body | 5.0.1+galaxy2 | 20.01 | |
| determines reads duplication rate with sequence-based and mapping-based strategies | 5.0.1+galaxy2 | 20.01 | |
| converts all types of RNA-seq data from .bam to .wig | 5.0.1+galaxy2 | 20.01 | |
| read coverage over gene body | 5.0.1+galaxy2 | 20.01 | |
| calculates how mapped reads were distributed over genome feature | 5.0.1+galaxy2 | 20.01 | |
| calculates hexamer (6mer) frequency for reads, genomes, and mRNA sequences | 5.0.1+galaxy2 | 20.01 | |
| calculates raw count and RPKM values for transcript at exon, intron, and mRNA level | 5.0.1+galaxy2 | 20.01 | |
| to check the nucleotide composition bias | 5.0.1+galaxy2 | 20.01 | |
| calculates the distribution of mismatches across reads | 5.0.1+galaxy2 | 20.01 | |
| speculates how RNA-seq were configured | 5.0.1+galaxy2 | 20.01 | |
| detects splice junctions from each subset and compares them to reference gene model | 5.0.1+galaxy2 | 20.01 | |
| calculates raw read count, FPM, and FPKM for each gene | 5.0.1+galaxy2 | 20.01 | |
| determines Phred quality score | 5.0.1+galaxy2 | 20.01 | |
| compares detected splice junctions to reference gene model | 5.0.1+galaxy2 | 20.01 | |
| reads mapping statistics for a provided BAM or SAM file. | 5.0.1+galaxy2 | 20.01 | |
| calculates the distributions of deleted nucleotides across reads | 5.0.1+galaxy2 | 20.01 | |
| determines GC% and read count | 5.0.1+galaxy2 | 20.01 | |
| calculates the distribution of inserted nucleotides across reads | 5.0.1+galaxy2 | 20.01 | |
| evaluates RNA integrity at a transcript level | 5.0.1+galaxy2 | 20.01 | |