Workflow Type: Galaxy

This workflow takes as input a list of single-read fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously. The counts are reprocess to be similar to HTSeq-count output. FPKM are computed with cufflinks. Coverage (per million mapped reads) are computed with bedtools on uniquely mapped reads.


ID Name Description Type
SR fastq input SR fastq input Should be a list of single-read RNA-seq fastqs
  • File[]
  • string
gtf gtf gtf compatible with the reference_genome. Mind the UCSC/Ensembl differences in chromosome naming
  • File
gtf with regions to exclude from FPKM normalization gtf with regions to exclude from FPKM normalization Could be a gtf with for example one entry for the chrM forward and one entry for the chrM reverse
  • File?
reference_genome reference_genome reference_genome
  • string
strandness strandness For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence
  • string


ID Name Description
6 Cutadapt (remove adapter + bad quality bases)
7 get reference_genome as text parameter
8 awk command from strand
9 bedtools orientation for forward coverage
10 bedtools orientation for reverse coverage
11 Get cufflinks strandess parameter
12 STAR: map and count
13 MultiQC
14 Extract gene counts
15 Keep only uniquely mapped reads
16 get scaling factor This step get 1 / millions of uniquely mapped reads
17 Compute FPKM
18 convert dataset to parameter param_value_from_file
19 Scaled Coverage both strands combined
20 Scaled Coverage positive
21 Scaled Coverage negative
22 convert both strands coverage to bigwig wig_to_bigWig
23 convert positive coverage to bigwig wig_to_bigWig
24 convert negative coverage to bigwig wig_to_bigWig


ID Name Description Type
output_log output_log n/a
  • File
reads_per_gene from STAR reads_per_gene from STAR n/a
  • File
mapped-reads mapped-reads n/a
  • File
MultiQC webpage MultiQC webpage n/a
  • File
MultiQC on input dataset(s): Stats MultiQC on input dataset(s): Stats n/a
  • File
HTS count like output HTS count like output n/a
  • File
transcripts_expression transcripts_expression n/a
  • File
genes_expression genes_expression n/a
  • File
both strands coverage both strands coverage n/a
  • File
positive strand coverage positive strand coverage n/a
  • File
negative strand coverage negative strand coverage n/a
  • File

Version History

v0.4 (latest) Created 17th Jan 2023 at 03:01 by WorkflowHub Bot

Updated to v0.4

Frozen v0.4 f49c5a7

v0.2 Created 1st Dec 2022 at 03:01 by WorkflowHub Bot

Updated to v0.2

Frozen v0.2 28b9493

v0.1 (earliest) Created 22nd Oct 2022 at 03:01 by WorkflowHub Bot

Updated to v0.1

Frozen v0.1 30a19f3
help Creators and Submitter
  • Lucille Delisle
Additional credit

Lucille Delisle


Views: 277

Created: 22nd Oct 2022 at 03:01

Last updated: 17th Jan 2023 at 03:01

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