Input dataset
output
Bowtie2
FASTQ file
output_unaligned_reads_l
output_unaligned_reads_r
output
Add or Replace Groups
SAM/BAM dataset to add or replace read groups in
outFile
Generate pileup
Select the BAM file to generate the pileup file for
Select a reference genome
output1
Depth of Coverage
BAM file 1 > BAM file
Using reference file
RefSeq Rod
output_per_locus_coverage
output_summary_sample
output_statistics_sample
output_interval_summary_sample
output_interval_statistics_sample
output_gene_summary_sample
output_gene_statistics_sample
output_cumulative_coverage_counts_sample
output_cumulative_coverage_proportions_sample
output_summary_readgroup
output_statistics_readgroup
output_interval_summary_readgroup
output_interval_statistics_readgroup
output_gene_summary_readgroup
output_gene_statistics_readgroup
output_cumulative_coverage_counts_readgroup
output_cumulative_coverage_proportions_readgroup
output_summary_library
output_statistics_library
output_interval_summary_library
output_interval_statistics_library
output_gene_summary_library
output_gene_statistics_library
output_cumulative_coverage_counts_library
output_cumulative_coverage_proportions_library
output_log
Filter pileup
Select dataset
out_file1
Filter
Filter
out_file1
Pileup-to-Interval
Choose a pileup file to condense:
output
Summary Statistics
Summary statistics on
out_file1
Base Coverage
Compute coverage for
output