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.
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.

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