Pipeline steps

• Quality statistics (fastq level)
  • fastqc
  • htseq-qa
  • fastp (fastqc, htseq-qa)
• Remove adapters (5', 3' polyA tail)
  • cutadapt
  • fastp
• Create index for mapping
  • STAR
• Map reads
  • STAR
    • add feature two-pass mode
    • multimappers
    • End to End
• Quality statistics (bam level)
  • ALFA (https://github.com/biocompibens/ALFA)
• Estimate gene/transcript expression
  • salmon on fastq file
  • kallisto on fastq file
• Summary
  • Create gene expression table of
  • TPM
  • Normalized (raw) reads
  • multiqc

added Doing label

assigned to @gypas

assigned to @katsanto and unassigned @gypas

assigned to @gypas and unassigned @katsanto

assigned to @katsanto and unassigned @gypas

unassigned @katsanto

assigned to @herrmchr

assigned to @gypas and unassigned @herrmchr

marked the checklist item Quality statistics (fastq level) as completed

marked the checklist item Quality statistics (fastq level) as incomplete

changed the description

Example

configfile: "config.yaml"

################################################################################
### python modules
################################################################################

import os
import sys
import pandas as pd

################################################################################
### Custom functions
################################################################################

def get_samples():
    design_table = pd.read_csv(config["samples"], sep="\t", header=0)
    return list(design_table["sample"])

def get_fq_1(wildcards):
    design_table = pd.read_csv(config["samples"], sep="\t", index_col="sample")
    return str(design_table.loc[wildcards.sample]["fq1"])

def get_fq_2(wildcards):
    design_table = pd.read_csv(config["samples"], sep="\t", index_col="sample")
    return str(design_table.loc[wildcards.sample]["fq2"])

assigned to @katsanto and unassigned @gypas

marked the checklist item fastqc as completed

marked the checklist item htseq-qa as completed

marked the checklist item cutadapt as completed

marked the checklist item STAR as completed

marked the checklist item STAR as incomplete

changed the description

marked the checklist item STAR as completed

marked the checklist item STAR as completed

changed the description

marked the checklist item multimappers as completed

marked the checklist item End to End as completed

marked the checklist item salmon on fastq file as completed

marked the checklist item kallisto on fastq file as completed

mentioned in issue #40 (closed)

marked the checklist item Create index for mapping as completed

marked the checklist item Estimate gene/transcript expression as completed

Many rules are available but not yet wired. Rules that are not yet available have their own issues (e.g., ALFA #18 (closed), MultiQC #23 (closed)), therefore close this issue once available rules have been wired.

marked the checklist item fastp as completed

marked the checklist item Quality statistics (fastq level) as completed

marked the checklist item fastp as completed

marked the checklist item Remove adapters (5', 3' polyA tail) as completed

Well, perhaps check if there is anything else that is not taken care of in other issues (two-pass mode, summary...). If so, open specific issues as otherwise it is difficult to resolve this "meta issue"

mentioned in issue #48 (closed)

closed via commit ca9a2bb4

mentioned in commit ca9a2bb4

removed Doing label