Galaxy | Accessible Workflow | ChIP-Seq Analysis for heatmaps

ChIP-Seq Analysis for heatmaps

Annotation:

Step	Annotation
Step 1: Input dataset WT_Input.fastq select at runtime
Step 2: Input dataset WT_IP.fastq select at runtime
Step 3: Input dataset elg1_INPUT.fastq select at runtime
Step 4: Input dataset elg1_IP.fastq select at runtime
Step 5: Input dataset Late Origins.bed select at runtime
Step 6: Input dataset Early origins.bed select at runtime
Step 7: Map with BWA Will you select a reference genome from your history or use a built-in index? Use a built-in genome index Using reference genome sacCer3 Select input type Single fastq Select fastq dataset Output dataset 'output' from step 1 Set advanced single end options? Do not set Set read groups information? Set read groups (SAM/BAM specification) Auto-assign True Auto-assign True Platform/technology used to produce the reads (PL) ILLUMINA Auto-assign True Sequencing center that produced the read (CN) Empty. Description (DS) Empty. Date that run was produced (DT) Empty. Flow order (FO) Empty. The array of nucleotide bases that correspond to the key sequence of each read (KS) Empty. Programs used for processing the read group (PG) Empty. Predicted median insert size (PI) Not available. Platform unit (PU) Empty. Select analysis mode 1.Simple Illumina mode Job Resource Parameters Use default job resource parameters
Step 8: Map with BWA Will you select a reference genome from your history or use a built-in index? Use a built-in genome index Using reference genome sacCer3 Select input type Single fastq Select fastq dataset Output dataset 'output' from step 2 Set advanced single end options? Do not set Set read groups information? Set read groups (SAM/BAM specification) Auto-assign True Auto-assign True Platform/technology used to produce the reads (PL) ILLUMINA Auto-assign True Sequencing center that produced the read (CN) Empty. Description (DS) Empty. Date that run was produced (DT) Empty. Flow order (FO) Empty. The array of nucleotide bases that correspond to the key sequence of each read (KS) Empty. Programs used for processing the read group (PG) Empty. Predicted median insert size (PI) Not available. Platform unit (PU) Empty. Select analysis mode 1.Simple Illumina mode Job Resource Parameters Use default job resource parameters
Step 9: Map with BWA Will you select a reference genome from your history or use a built-in index? Use a built-in genome index Using reference genome sacCer3 Select input type Single fastq Select fastq dataset Output dataset 'output' from step 3 Set advanced single end options? Do not set Set read groups information? Set read groups (SAM/BAM specification) Auto-assign True Auto-assign True Platform/technology used to produce the reads (PL) ILLUMINA Auto-assign True Sequencing center that produced the read (CN) Empty. Description (DS) Empty. Date that run was produced (DT) Empty. Flow order (FO) Empty. The array of nucleotide bases that correspond to the key sequence of each read (KS) Empty. Programs used for processing the read group (PG) Empty. Predicted median insert size (PI) Not available. Platform unit (PU) Empty. Select analysis mode 1.Simple Illumina mode Job Resource Parameters Use default job resource parameters
Step 10: Map with BWA Will you select a reference genome from your history or use a built-in index? Use a built-in genome index Using reference genome sacCer3 Select input type Single fastq Select fastq dataset Output dataset 'output' from step 4 Set advanced single end options? Do not set Set read groups information? Set read groups (SAM/BAM specification) Auto-assign True Auto-assign True Platform/technology used to produce the reads (PL) ILLUMINA Auto-assign True Sequencing center that produced the read (CN) Empty. Description (DS) Empty. Date that run was produced (DT) Empty. Flow order (FO) Empty. The array of nucleotide bases that correspond to the key sequence of each read (KS) Empty. Programs used for processing the read group (PG) Empty. Predicted median insert size (PI) Not available. Platform unit (PU) Empty. Select analysis mode 1.Simple Illumina mode Job Resource Parameters Use default job resource parameters
Step 11: Filter SAM or BAM, output SAM or BAM SAM or BAM file to filter Output dataset 'bam_output' from step 7 Header in output Include header Minimum MAPQ quality score 20 Filter on bitwise flag no Select alignments from Library Empty. Select alignments from Read Group Empty. Output alignments overlapping the regions in the BED file select at runtime Use inverse selection False Select regions (only used when the input is in BAM format) Empty. Select the output format BAM (-b)
Step 12: Filter SAM or BAM, output SAM or BAM SAM or BAM file to filter Output dataset 'bam_output' from step 8 Header in output Include header Minimum MAPQ quality score 20 Filter on bitwise flag no Select alignments from Library Empty. Select alignments from Read Group Empty. Output alignments overlapping the regions in the BED file select at runtime Use inverse selection False Select regions (only used when the input is in BAM format) Empty. Select the output format BAM (-b)
Step 13: Filter SAM or BAM, output SAM or BAM SAM or BAM file to filter Output dataset 'bam_output' from step 9 Header in output Include header Minimum MAPQ quality score 20 Filter on bitwise flag no Select alignments from Library Empty. Select alignments from Read Group Empty. Output alignments overlapping the regions in the BED file select at runtime Use inverse selection False Select regions (only used when the input is in BAM format) Empty. Select the output format BAM (-b)
Step 14: Filter SAM or BAM, output SAM or BAM SAM or BAM file to filter Output dataset 'bam_output' from step 10 Header in output Include header Minimum MAPQ quality score 20 Filter on bitwise flag no Select alignments from Library Empty. Select alignments from Read Group Empty. Output alignments overlapping the regions in the BED file select at runtime Use inverse selection False Select regions (only used when the input is in BAM format) Empty. Select the output format BAM (-b)
Step 15: bamCompare First BAM/CRAM file (e.g. treated sample) Output dataset 'output1' from step 12 Second BAM/CRAM file (e.g. control sample) Output dataset 'output1' from step 11 Bin size in bases 50 Method to use for scaling the largest sample to the smallest signal extraction scaling (SES), check with plotFingerprint before using it! Length in bases used to sample the genome and compute the size or scaling factors. 100 Number of samplings taken from the genome to compute the scaling factors 100000 How to compare the two files Compute log2 of the number of reads ratio Pseudocount 1.0 Compute an exact scaling factor False Coverage file format bigwig Region of the genome to limit the operation to Empty. Show advanced options no Job Resource Parameters Use default job resource parameters
Step 16: bamCompare First BAM/CRAM file (e.g. treated sample) Output dataset 'output1' from step 14 Second BAM/CRAM file (e.g. control sample) Output dataset 'output1' from step 13 Bin size in bases 50 Method to use for scaling the largest sample to the smallest signal extraction scaling (SES), check with plotFingerprint before using it! Length in bases used to sample the genome and compute the size or scaling factors. 100 Number of samplings taken from the genome to compute the scaling factors 100000 How to compare the two files Compute log2 of the number of reads ratio Pseudocount 1.0 Compute an exact scaling factor False Coverage file format bigwig Region of the genome to limit the operation to Empty. Show advanced options no Job Resource Parameters Use default job resource parameters
Step 17: computeMatrix Select regions Select regions 1 Regions to plot Output dataset 'output' from step 5 Sample order matters No Score file Output dataset 'outFileName' from step 15 computeMatrix has two main output options scale-regions Distance in bases to which all regions are going to be fit 500 Set distance up- and downstream of the given regions yes Distance upstream of the region start position 20000 Distance downstream of the region end position 20000 Number of bases within the gene body at the 5-prime end to exclude from scaling. 0 Number of bases within the gene body at the 3-prime end to exclude from scaling. 0 Show advanced output settings yes Save the matrix of values underlying the heatmap False Save the regions after skipping zeros or min/max threshold values False Show advanced options yes Length, in bases, of non-overlapping bins used for averaging the score over the regions length 50 Sort regions maintain the same ordering as the input files Method used for sorting mean Define the type of statistic that should be displayed. mean Convert missing values to 0? False Skip zeros False Minimum threshold Not available. Maximum threshold Not available. Scaling factor Not available. Labels for the samples (each bigwig) Empty. Use a metagene model False transcript designator transcript exon designator exon transcriptID key designator transcript_id Blacklisted regions in BED/GTF format select at runtime Job Resource Parameters Use default job resource parameters
Step 18: computeMatrix Select regions Select regions 1 Regions to plot Output dataset 'output' from step 6 Sample order matters No Score file Output dataset 'outFileName' from step 15 computeMatrix has two main output options scale-regions Distance in bases to which all regions are going to be fit 500 Set distance up- and downstream of the given regions yes Distance upstream of the region start position 20000 Distance downstream of the region end position 20000 Number of bases within the gene body at the 5-prime end to exclude from scaling. 0 Number of bases within the gene body at the 3-prime end to exclude from scaling. 0 Show advanced output settings no Show advanced options no Job Resource Parameters Use default job resource parameters
Step 19: computeMatrix Select regions Select regions 1 Regions to plot Output dataset 'output' from step 6 Sample order matters No Score file Output dataset 'outFileName' from step 16 computeMatrix has two main output options scale-regions Distance in bases to which all regions are going to be fit 500 Set distance up- and downstream of the given regions yes Distance upstream of the region start position 20000 Distance downstream of the region end position 20000 Number of bases within the gene body at the 5-prime end to exclude from scaling. 0 Number of bases within the gene body at the 3-prime end to exclude from scaling. 0 Show advanced output settings yes Save the matrix of values underlying the heatmap False Save the regions after skipping zeros or min/max threshold values False Show advanced options yes Length, in bases, of non-overlapping bins used for averaging the score over the regions length 50 Sort regions maintain the same ordering as the input files Method used for sorting mean Define the type of statistic that should be displayed. mean Convert missing values to 0? False Skip zeros False Minimum threshold Not available. Maximum threshold Not available. Scaling factor Not available. Labels for the samples (each bigwig) Empty. Use a metagene model False transcript designator transcript exon designator exon transcriptID key designator transcript_id Blacklisted regions in BED/GTF format select at runtime Job Resource Parameters Use default job resource parameters
Step 20: computeMatrix Select regions Select regions 1 Regions to plot Output dataset 'output' from step 5 Sample order matters No Score file Output dataset 'outFileName' from step 16 computeMatrix has two main output options scale-regions Distance in bases to which all regions are going to be fit 500 Set distance up- and downstream of the given regions yes Distance upstream of the region start position 20000 Distance downstream of the region end position 20000 Number of bases within the gene body at the 5-prime end to exclude from scaling. 0 Number of bases within the gene body at the 3-prime end to exclude from scaling. 0 Show advanced output settings no Show advanced options no Job Resource Parameters Use default job resource parameters
Step 21: plotHeatmap Matrix file from the computeMatrix tool Output dataset 'outFileName' from step 17 Show advanced output settings yes Image file format png Image dpi 400 Save the matrix of values underlying the heatmap False Save the regions after skipping zeros or min/max threshold values False Show advanced options yes Sort regions descending order Method used for sorting mean Type of statistic that should be plotted in the summary image above the heatmap mean Missing data color black Colormap to use for each samples Colormap to use for each sample 1 Color map to use for the heatmap jet Alpha channel (transparency) 1.0 List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas Empty. Minimum value for the heatmap intensities Empty. Maximum value for the heatmap intensities Empty. Minimum value for the Y-axis of the summary plot. Leave empty for automatic values 0.0 Maximum value for Y-axis of the summary plot. Leave empty for automatic values 2.0 The x-axis label Empty. The y-axis label for the top panel Empty. Heatmap width in cm 7.5 Heatmap height in cm 25.0 What to show summary plot, heatmap and colorbar Label for the region start S Label for the region end E Reference point label Empty. Labels for the samples (each bigwig) plotted Empty. Labels for the regions plotted in the heatmap Empty. Title of the plot Empty. Rotation of the X-axis labels (in degrees) 0 Make one plot per group of regions True Did you compute the matrix with more than one groups of regions? Yes, I used multiple groups of regions
Step 22: plotHeatmap Matrix file from the computeMatrix tool Output dataset 'outFileName' from step 18 Show advanced output settings yes Image file format png Image dpi 400 Save the matrix of values underlying the heatmap False Save the regions after skipping zeros or min/max threshold values False Show advanced options yes Sort regions descending order Method used for sorting mean Type of statistic that should be plotted in the summary image above the heatmap mean Missing data color black Colormap to use for each samples Colormap to use for each sample 1 Color map to use for the heatmap jet Alpha channel (transparency) 1.0 List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas Empty. Minimum value for the heatmap intensities Empty. Maximum value for the heatmap intensities Empty. Minimum value for the Y-axis of the summary plot. Leave empty for automatic values 0.0 Maximum value for Y-axis of the summary plot. Leave empty for automatic values 2.0 The x-axis label Empty. The y-axis label for the top panel Empty. Heatmap width in cm 7.5 Heatmap height in cm 25.0 What to show summary plot, heatmap and colorbar Label for the region start S Label for the region end E Reference point label Empty. Labels for the samples (each bigwig) plotted Empty. Labels for the regions plotted in the heatmap Empty. Title of the plot Empty. Rotation of the X-axis labels (in degrees) 0 Make one plot per group of regions False Did you compute the matrix with more than one groups of regions? Yes, I used multiple groups of regions
Step 23: plotHeatmap Matrix file from the computeMatrix tool Output dataset 'outFileName' from step 19 Show advanced output settings yes Image file format png Image dpi 400 Save the matrix of values underlying the heatmap False Save the regions after skipping zeros or min/max threshold values False Show advanced options yes Sort regions descending order Method used for sorting mean Type of statistic that should be plotted in the summary image above the heatmap mean Missing data color black Colormap to use for each samples Colormap to use for each sample 1 Color map to use for the heatmap jet Alpha channel (transparency) 1.0 List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas Empty. Minimum value for the heatmap intensities Empty. Maximum value for the heatmap intensities Empty. Minimum value for the Y-axis of the summary plot. Leave empty for automatic values 0.0 Maximum value for Y-axis of the summary plot. Leave empty for automatic values 2.0 The x-axis label Empty. The y-axis label for the top panel Empty. Heatmap width in cm 7.5 Heatmap height in cm 25.0 What to show summary plot, heatmap and colorbar Label for the region start S Label for the region end E Reference point label Empty. Labels for the samples (each bigwig) plotted Empty. Labels for the regions plotted in the heatmap Empty. Title of the plot Empty. Rotation of the X-axis labels (in degrees) 0 Make one plot per group of regions False Did you compute the matrix with more than one groups of regions? Yes, I used multiple groups of regions
Step 24: plotHeatmap Matrix file from the computeMatrix tool Output dataset 'outFileName' from step 20 Show advanced output settings yes Image file format png Image dpi 400 Save the matrix of values underlying the heatmap False Save the regions after skipping zeros or min/max threshold values False Show advanced options yes Sort regions descending order Method used for sorting mean Type of statistic that should be plotted in the summary image above the heatmap mean Missing data color black Colormap to use for each samples Colormap to use for each sample 1 Color map to use for the heatmap jet Alpha channel (transparency) 1.0 List of colors for each heatmap. Separate lists by spaces and the colors in the list by comas Empty. Minimum value for the heatmap intensities Empty. Maximum value for the heatmap intensities Empty. Minimum value for the Y-axis of the summary plot. Leave empty for automatic values 0.0 Maximum value for Y-axis of the summary plot. Leave empty for automatic values 2.0 The x-axis label Empty. The y-axis label for the top panel Empty. Heatmap width in cm 7.5 Heatmap height in cm 25.0 What to show summary plot, heatmap and colorbar Label for the region start S Label for the region end E Reference point label Empty. Labels for the samples (each bigwig) plotted Empty. Labels for the regions plotted in the heatmap Empty. Title of the plot Empty. Rotation of the X-axis labels (in degrees) 0 Make one plot per group of regions True Did you compute the matrix with more than one groups of regions? Yes, I used multiple groups of regions

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ChIP-Seq Analysis for heatmaps

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