Up: Components summary
Up: Components summary
Author
Alejandra Cervera| Component | Version | Inputs | Outputs | Description |
|---|---|---|---|---|
| AdaptorRemoval | 2.1 | reads, tags, overSeqs | arrayOut, removalLog, predictLog | Removes tags from the reads in fastq/fasta files. |
| AligFilterFlag | 1.1 | alignment | splitAlignments1, splitAlignments2 | Allows to filter SAM files with alignments using the flag field. |
| AligFilterMatches | 1.0 | accepted_hits | dataOut1, dataOut2 | Allows filtering of alignments in BAM/SAM files, mainly output from Tophat. |
| AlignStats | 1.2 | alignment, reference, annotation, refgene, chromsize, log | report, stats | Evaluate sequencing data, especially RNA-seq data quality using RSeQC. |
| Cuffcompare | 1.0 | arrayIn, reference_annotation, seq_dir | arrayOut | Cufflinks includes a program that you can use to help analyze the transfrags you assemble. |
| Cuffdiff | 1.0 | transcripts, array, mask, genome | isoforms, genes, cds, tss_groups, isoform_exp, gene_exp, cds_exp, tss_group_exp, splicing, cds_output, promoters | Cufflinks includes a program, "Cuffdiff", that you can use to find significant changes in transcript expression, splicing, and promoter use. |
| Cufflinks | 1.0 | alignment, reference_annotation1, reference_annotation2, mask, genome | transcripts, isoforms, genes | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. |
| Cuffmerge | 1.0 | arrayIn, ref_gtf, ref_seq | merged | Cufflinks includes a script called cuffmerge that you can use to merge together several Cufflinks assemblies. |
| DEan | 0.4 | expr, treatment | array, diffExpr | Performs differential expression analyses in R between pairs of sample groups using up to 4 methods: DESeq, DESeq2, EdgeR, and upper-quartile normalization with t-test. |
| DiffExprSeq | 1.0 | exonCounts, geneCounts, annotation, conditions | exon, gene | For differential expression at gene and exon level of RNA-Seq data. |
| ExpressionQuantifier | 2.0 | alignment, reference, referenceFolder, annotation, mask, array | folder, genes, isoforms | Quantifies expression from a bam file from RNA-Seq. |
| ExpressionStats | 0.1 | expr, ref, geneSet, bodyMap | stats, statsArray, report | Given an expression matrix and a CSV containing sample IDs and treatment groups, calculate basic statistics by treatment group: mean, median, and standard deviation of genes. |
| ExprTable | 1.1 | array, auxiliary | table, log2, topHits, plots | Generates an expression table from individual samples expression files. It was created with genes.fpkm_tracking and isoforms.fpkm_tracking files from Cufflinks in mind, but it can be used to summarize in one table any group of expression files that have an id column common to all files and the expression values. |
| ExprTableReport | 1.0 | expr, ref, colLabels, annotation, geneSet, bodyMap | table, expressed, document, report | Generates expression statistics into an HTML report. |
| FastQC | 2.0 | read, mate | summary, report, extra, folder | Short reads quality control for high-throughput sequencing data. |
| FusionGenes | 1.0 | in | out | Allows filtering of alignments in BAM/SAM files, mainly output from Tophat. |
| HTSeqBam2Counts | 1.0 | alignments, annotationGTF, annotationGFF | exon, gene, annotation | For obtaining read counts at gene and exon level from RNA-Seq alignment files. |
| QCFasta | 5.0 | reads, mates, fastQCfolders, adapter | qcReads, qcMates, report, table, qcUnpairedReads, qcUnpairedMates | Quality control function for high-throughput sequencing data. |
| Star2Pass | 1.0 | reference, reads, mates, genome, annotation, parameterFile, custom | folder, alignments, spliceJunctions | Runs STAR aligner in two pass mode for an array of samples together. |
| Trimmomatic | 2.1 | read, mate, adapter | trimmedReads, stdout, stats, log | Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data. |