ncRNA analysis single-end v 4.0


StepAnnotation
Step 1: Input dataset collection
select at runtime
Step 2: Input dataset
select at runtime
Step 3: Input dataset collection
select at runtime
Step 4: Input dataset
select at runtime
Step 5: FastQC
Output dataset 'output' from step 1
select at runtime
select at runtime
select at runtime
False
Not available.
7
Use default job resource parameters
Step 6: HISAT2
Use a genome from history
Output dataset 'output' from step 2
Single-end
Output dataset 'output' from step 1
Unstranded
Summary Options:
True
True
Advanced Options:
Use default values
Use default values
Use default values
Use default values
Use default values
Use default values
Use default values
Use default job resource parameters
Step 7: FastQC
Output dataset 'output' from step 3
select at runtime
select at runtime
select at runtime
False
Not available.
7
Use default job resource parameters
Step 8: HISAT2
Use a genome from history
Output dataset 'output' from step 2
Single-end
Output dataset 'output' from step 3
Unstranded
Summary Options:
True
True
Advanced Options:
Use default values
Use default values
Use default values
Use default values
Use default values
Use default values
Use default values
Use default job resource parameters
Step 9: Convert
Whitespaces
Output dataset 'output' from step 4
True
True
Step 10: Filter
Output dataset 'output_alignments' from step 6
Conditions
Condition 1
Filters
Filter 1
mapQuality
>=10
False
Step 11: Filter
Output dataset 'output_alignments' from step 8
Conditions
Condition 1
Filters
Filter 1
mapQuality
>=10
False
Step 12: Text transformation
Output dataset 'out_file1' from step 9
s/#.*$//g
Hide Advanced Options
Step 13: featureCounts
Output dataset 'out_file1' from step 10
Unstranded
in your history
Output dataset 'output' from step 4
Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)
False
Options for paired-end reads:
Disabled; all reads/mates will be counted individually
False
True
Advanced options:
noncoding_exon
ID
False
False
Disabled; multi-mapping reads are excluded (default)
12
False
False
False
False
1
0
0
0
0
Leave the read as it is
False
False
False
False
Use default job resource parameters
Step 14: featureCounts
Output dataset 'out_file1' from step 11
Unstranded
in your history
Output dataset 'output' from step 4
Gene-ID "\t" read-count (MultiQC/DESeq2/edgeR/limma-voom compatible)
False
Options for paired-end reads:
Disabled; all reads/mates will be counted individually
False
True
Advanced options:
noncoding_exon
ID
False
False
Disabled; multi-mapping reads are excluded (default)
12
False
False
False
False
1
0
0
0
0
Leave the read as it is
False
False
False
False
Use default job resource parameters
Step 15: Text reformatting
Output dataset 'output' from step 12
BEGIN{} {match($9,/ID=([^ ]+);/,a); print $1,$2,$3,$4,$5,$6,$7,$8,a[1]} END{}
Step 16: Column join
Output dataset 'output_short' from step 13
1
0
False
Empty.
Nothing selected.
Step 17: DESeq2
Factors
Factor 1
sample
Factor levels
Factor level 1
test
Output dataset 'output_short' from step 14
Factor level 2
control
Output dataset 'output_short' from step 13
select at runtime
True
Count data (e.g. from HTSeq-count, featureCounts or StringTie)
True
True
False
parametric
False
False
False
Use default job resource parameters
Step 18: Column join
Output dataset 'output_short' from step 14
1
0
False
Empty.
Nothing selected.
Step 19: Filter
Output dataset 'deseq_out' from step 17
c7 <= 0.05
0
Step 20: Join
Output dataset 'tabular_output' from step 16
1
Output dataset 'tabular_output' from step 18
1
Both 1st & 2nd file.
True
False
0
Step 21: Compare two Datasets
Output dataset 'outfile' from step 15
9
Output dataset 'out_file1' from step 19
1
Matching rows of 1st dataset
Step 22: Build list
Datasets
Dataset 1
Output dataset 'output' from step 20
Index
Dataset 2
Output dataset 'counts_out' from step 17
Index
Dataset 3
Output dataset 'deseq_out' from step 17
Index
Step 23: Text reformatting
Output dataset 'out_file1' from step 21
BEGIN{} {$9="ID=" $9 ";" }1 END{}
Step 24: Column join
Output dataset 'output' from step 22
1
0
True
.
Nothing selected.