Galaxy | Accessible Workflow | RNAseq_pairedend_pairedcollection

RNAseq_pairedend_pairedcollection

Annotation:

Step	Annotation
Step 1: Input dataset collection input select at runtime
Step 2: Input dataset P. berghei reference genome select at runtime
Step 3: Input dataset P.berg select at runtime
Step 4: Trim Galore! Is this library paired- or single-end? Paired Collection Select a paired collection Output dataset 'output' from step 1 Adapter sequence to be trimmed Automatic detection Trims 1 bp off every read from its 3' end. False Remove N bp from the 3' end of read 1 Not available. Remove N bp from the 3' end of read 2 Not available. Trim Galore! advanced settings Use defaults RRBS specific settings Use defaults (no RRBS)	Remove illumina adapter sequences.
Step 5: FastQC Short read data from your current history Output dataset 'trimmed_reads_paired_collection' from step 4 Contaminant list select at runtime Submodule and Limit specifing file select at runtime
Step 6: HISAT2 Source for the reference genome Use a genome from history Select the reference genome Output dataset 'output' from step 2 Is this a single or paired library Paired-end Dataset Collection Paired Collection Output dataset 'trimmed_reads_paired_collection' from step 4 Specify strand information Unstranded Paired-end options Use default values Summary Options: Output alignment summary in a more machine-friendly style. False Print alignment summary to a file. False Advanced Options: Input options Use default values Alignment options Use default values Scoring options Use default values Spliced alignment options Use default values Reporting options Use default values Output options Use default values Other options Use default values Job Resource Parameters Use default job resource parameters
Step 7: featureCounts Alignment file Output dataset 'output_alignments' from step 6 Specify strand information Unstranded Gene annotation file in your history Gene annotation file Output dataset 'output' from step 3 Output format Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible) Create gene-length file False Options for paired-end reads: Count fragments instead of reads Disabled; all reads/mates will be counted individually Only allow fragments with both reads aligned False Exclude chimeric fragments True Advanced options: GFF feature type filter gene GFF gene identifier ID On feature level False Allow read to contribute to multiple features False Count multi-mapping reads/fragments Disabled; multi-mapping reads are excluded (default) Minimum mapping quality per read 12 Exon-exon junctions False Long reads False Count reads by read group False Largest overlap False Minimum bases of overlap 1 Minimum fraction (of read) overlapping a feature 0 Minimum fraction (of feature) overlapping a read 0 Read 5' extension 0 Read 3' extension 0 Reduce read to single position Leave the read as it is Only count primary alignments False Ignore reads marked as duplicate False Annotates the alignment file with 'XS:Z:'-tags to described per read or read-pair the corresponding assigned feature(s). False Ignore unspliced alignments False Job Resource Parameters Use default job resource parameters	GFF gene identifer changed to 'ID' from 'geneID' because of the formatting of the particular .bam files. Check ninth column of the bam files for which identifier is being used.

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t_little

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