MultiQC andInitialisation of GRCh38

Init

Preparing GRCh38-aligned data for analysis

Authors

Affiliations

Gavin Kelly ^[Analyst]

Francis Crick Institute

BABS ^{[Development]}

Francis Crick Institute

Gavin Kelly ^{[Developer,Statistical Metholodogy]}

Francis Crick Institute

Setting	Value
section	Initialisation
res_dir	results/v9.9.9
VERSION	v9.9.9
TAG	_v9.9.9-00eb166
staging_dir	staging
file_col	ID
name_col	sample_name
metadata	extdata/metadata_GRCh38.csv
counts	extdata/genes.results/GRCh38/
alignment	GRCh38
spec
specname
script	staging/00_init_GRCh38.qmd

1 MultiQC

MultiQC report for GRCh38

2 Using Nextflow output

Setting	Value
Data-source Type	Nextflow rsem
Source file1	extdata/genes.results/GRCh38//SRR1039508.genes.results
Source file2	extdata/genes.results/GRCh38//SRR1039509.genes.results
Source file3	extdata/genes.results/GRCh38//SRR1039512.genes.results
Source file4	extdata/genes.results/GRCh38//SRR1039513.genes.results
Source file5	extdata/genes.results/GRCh38//SRR1039516.genes.results
Source file6	extdata/genes.results/GRCh38//SRR1039517.genes.results
Source file7	extdata/genes.results/GRCh38//SRR1039520.genes.results
Source file8	extdata/genes.results/GRCh38//SRR1039521.genes.results
genome_fasta	/nemo/svc/reference/Genomics/babs/homo_sapiens/ensembl/GRCh38/release-95/genome/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa
gtf	/nemo/svc/reference/Genomics/babs/homo_sapiens/ensembl/GRCh38/release-95/gtf/Homo_sapiens.GRCh38.95.gtf
org.db	org.Hs.eg.db
nfcore	-profile crick -resume -r 3.10.1
universal	yes
strandedness	auto
aligner	star_rsem
genome_fasta_md5	6ee1ec578b2b6495eb7da26885d0a496
gtf_md5	fb0c91f8e0cc49996571f8d09f1811ca
keytype	ENSEMBL

It looks like you are importing RSEM genes.results files, setting txIn=FALSE

reading in files with read_tsv

1 2 3 4 5 6 7 8 
using counts and average transcript lengths from tximport
Loading required package: AnnotationDbi

Attaching package: 'AnnotationDbi'

The following object is masked from 'package:dplyr':

    select

'select()' returned 1:many mapping between keys and columns
'select()' returned 1:many mapping between keys and columns