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Published Workflows | chanaka | RNASeq Analysis

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Galaxy Workflow ' RNASeq Analysis'

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Step	Annotation
Step 1: Input dataset asp5_leaf_read1.P001.fq select at runtime	asp5_leaf_read1.P001.fq
Step 2: Input dataset asp5_leaf_read2.P001.fq select at runtime	asp5_leaf_read2.P001.fq
Step 3: Input dataset asp5_xylem_read1.P001.fq select at runtime	asp5_xylem_read1.P001.fq
Step 4: Input dataset asp5_xylem_read2.P001.fq select at runtime	asp5_xylem_read2.P001.fq
Step 5: PopGenIE random fastq extract tool Input pair 1 Output dataset 'output' from step 1 Input pair 2 Output dataset 'output' from step 2
Step 6: PopGenIE random fastq extract tool Input pair 1 Output dataset 'output' from step 3 Input pair 2 Output dataset 'output' from step 4
Step 7: FASTQ Groomer File to groom Output dataset 'output1' from step 5 Input FASTQ quality scores type Sanger Advanced Options Hide Advanced Options
Step 8: FASTQ Groomer File to groom Output dataset 'output2' from step 5 Input FASTQ quality scores type Sanger Advanced Options Hide Advanced Options
Step 9: FASTQ Groomer File to groom Output dataset 'output1' from step 6 Input FASTQ quality scores type Sanger Advanced Options Hide Advanced Options
Step 10: FASTQ Groomer File to groom Output dataset 'output2' from step 6 Input FASTQ quality scores type Sanger Advanced Options Hide Advanced Options
Step 11: Trim sequences Library to clip Output dataset 'output_file' from step 7 First base to keep 10 Last base to keep 90
Step 12: Fastqc: Fastqc QC Short read data from your current history Output dataset 'output_file' from step 7 Title for the output file - to remind you what the job was for FastQC Contaminant list select at runtime
Step 13: Trim sequences Library to clip Output dataset 'output_file' from step 8 First base to keep 10 Last base to keep 90
Step 14: Fastqc: Fastqc QC Short read data from your current history Output dataset 'output_file' from step 8 Title for the output file - to remind you what the job was for FastQC Contaminant list select at runtime
Step 15: Fastqc: Fastqc QC Short read data from your current history Output dataset 'output_file' from step 9 Title for the output file - to remind you what the job was for FastQC Contaminant list select at runtime
Step 16: Trim sequences Library to clip Output dataset 'output_file' from step 9 First base to keep 10 Last base to keep 90
Step 17: Fastqc: Fastqc QC Short read data from your current history Output dataset 'output_file' from step 10 Title for the output file - to remind you what the job was for FastQC Contaminant list select at runtime
Step 18: Trim sequences Library to clip Output dataset 'output_file' from step 10 First base to keep 10 Last base to keep 90
Step 19: Tophat Will you select a reference genome from your history or use a built-in index? Use a built-in index Select a reference genome Populus_unmasked Is this library mate-paired? Paired-end RNA-Seq FASTQ file Output dataset 'output' from step 11 RNA-Seq FASTQ file Output dataset 'output' from step 13 Mean Inner Distance between Mate Pairs 20 TopHat settings to use Commonly used
Step 20: Tophat Will you select a reference genome from your history or use a built-in index? Use a built-in index Select a reference genome Populus_unmasked Is this library mate-paired? Paired-end RNA-Seq FASTQ file Output dataset 'output' from step 16 RNA-Seq FASTQ file Output dataset 'output' from step 18 Mean Inner Distance between Mate Pairs 20 TopHat settings to use Commonly used
Step 21: Cufflinks SAM or BAM file of aligned RNA-Seq reads Output dataset 'accepted_hits' from step 19 Max Intron Length 300000 Min Isoform Fraction 0.05 Pre MRNA Fraction 0.05 Perform quartile normalization No Use Reference Annotation No Perform Bias Correction No Set Parameters for Paired-end Reads? (not recommended) No
Step 22: Cufflinks SAM or BAM file of aligned RNA-Seq reads Output dataset 'accepted_hits' from step 20 Max Intron Length 300000 Min Isoform Fraction 0.05 Pre MRNA Fraction 0.05 Perform quartile normalization No Use Reference Annotation No Perform Bias Correction No Set Parameters for Paired-end Reads? (not recommended) No
Step 23: Cuffcompare GTF file produced by Cufflinks Output dataset 'assembled_isoforms' from step 21 Additional GTF Input Files Additional GTF Input Files 1 GTF file produced by Cufflinks Output dataset 'assembled_isoforms' from step 22 Use Reference Annotation Yes Reference Annotation select at runtime Ignore reference transcripts that are not overlapped by any transcript in input files False Use Sequence Data No
Step 24: Cuffdiff Transcripts Output dataset 'transcripts_combined' from step 23 Perform replicate analysis No SAM or BAM file of aligned RNA-Seq reads Output dataset 'accepted_hits' from step 19 SAM or BAM file of aligned RNA-Seq reads Output dataset 'accepted_hits' from step 20 False Discovery Rate 0.05 Min Alignment Count 1000 Perform quartile normalization No Perform Bias Correction No Set Parameters for Paired-end Reads? (not recommended) No

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chanaka

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Galaxy Workflow ' RNASeq Analysis'

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