Workflow Type: Galaxy
Stable

This workflow correspond to the Genome-wide alternative splicing analysis training. It allows to analyze isoform switching by making use of IsoformSwitchAnalyzeR.

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Inputs

ID Name Description Type
CPAT_header_tab n/a n/a
  • File
GRCh38_p13_genome_fa_gz n/a n/a
  • File
Input Dataset Collection n/a n/a
  • File
Pfam-A_hmm_dat_gz n/a n/a
  • File
Pfam-A_hmm_gz n/a n/a
  • File
active_site_dat_gz n/a n/a
  • File
gencode_v43_annotation_gtf_gz n/a n/a
  • File
gencode_v43_lncRNA_transcripts_fa_gz n/a n/a
  • File
gencode_v43_pc_transcripts_fa_gz n/a n/a
  • File
gencode_v43_transcripts_fa_gz n/a n/a
  • File

Steps

ID Name Description
10_Convert GTF to BED12 n/a n/a
11_fastp n/a n/a
12_Flatten collection n/a n/a
13_RNA STAR n/a n/a
14_FastQC n/a n/a
15_StringTie n/a n/a
16_Junction Annotation n/a n/a
17_Infer Experiment n/a n/a
18_Read Distribution n/a n/a
19_Gene Body Coverage (BAM) n/a n/a
20_Junction Saturation n/a n/a
21_MultiQC n/a n/a
22_Extract element identifiers n/a n/a
23_MultiQC n/a n/a
24_Search in textfiles n/a n/a
25_Filter collection n/a n/a
26_IsoformSwitchAnalyzeR n/a n/a
27_IsoformSwitchAnalyzeR n/a n/a
28_CPAT n/a n/a
29_PfamScan n/a n/a
30_Remove beginning n/a n/a
31_Text reformatting n/a n/a
32_Concatenate datasets n/a n/a
33_IsoformSwitchAnalyzeR n/a n/a
34_IsoformSwitchAnalyzeR n/a n/a

Version History

Version 4 (latest) Created 25th May 2023 at 22:57 by Cristóbal Gallardo

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Frozen Version-4 b79e689

Version 3 Created 25th May 2023 at 22:39 by Cristóbal Gallardo

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Frozen Version-3 ad0a0a5

Version 2 Created 24th May 2023 at 00:22 by Cristóbal Gallardo

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Frozen Version-2 2010989

Version 1 (earliest) Created 17th May 2023 at 12:21 by Cristóbal Gallardo

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Frozen Version-1 572676e
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Created: 17th May 2023 at 12:21

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