Input dataset
output
Input dataset
output
Input dataset
output
Input dataset
output
Input dataset
output
FastQC:Read QC
Short read data from your current history
Contaminant list
html_file
FastQC:Read QC
Short read data from your current history
Contaminant list
html_file
Tophat2
RNA-Seq FASTQ file, forward reads
RNA-Seq FASTQ file, reverse reads
align_summary
fusions
insertions
deletions
junctions
accepted_hits
FastQC:Read QC
Short read data from your current history
Contaminant list
html_file
FastQC:Read QC
Short read data from your current history
Contaminant list
html_file
Tophat2
RNA-Seq FASTQ file, forward reads
RNA-Seq FASTQ file, reverse reads
align_summary
fusions
insertions
deletions
junctions
accepted_hits
Cufflinks
SAM or BAM file of aligned RNA-Seq reads
Reference Annotation
Global model (for use in Trackster)
genes_expression
transcripts_expression
assembled_isoforms
total_map_mass
Merge BAM Files
First file
with file
output1
outlog
Cufflinks
SAM or BAM file of aligned RNA-Seq reads
Reference Annotation
Global model (for use in Trackster)
genes_expression
transcripts_expression
assembled_isoforms
total_map_mass
Cufflinks
SAM or BAM file of aligned RNA-Seq reads
Reference Annotation
Global model (for use in Trackster)
genes_expression
transcripts_expression
assembled_isoforms
total_map_mass
Cuffdiff
Transcripts
Condition 1 > Replicate 1 > Add replicate
Condition 2 > Replicate 1 > Add replicate
isoforms_read_group
genes_read_group
cds_read_group
tss_groups_read_group
splicing_diff
promoters_diff
cds_diff
cds_exp_fpkm_tracking
cds_fpkm_tracking
tss_groups_exp
tss_groups_fpkm_tracking
genes_exp
genes_fpkm_tracking
isoforms_exp
isoforms_fpkm_tracking
Filter
Filter
out_file1