Comments (2)
Whelp, I solved my own problem by actually reading the tximport
documentation for RSEM. In case it helps someone else, here's the code snippet to get the lengths from the RSEM output from nf-core/rnaseq:
library(tximport)
files = Sys.glob('star_rsem/*.genes.results')
names = c()
for (filename in files) { names = c(names, strsplit(strsplit(filename, '/')[[1]][2], '.genes')[[1]][1]) }
names(files) = names
txi.rsem <- tximport(files, type = "rsem", txIn = FALSE, txOut = FALSE)
head(txi.rsem$length)
write.table(txi.rsem$length, 'rsem_gene_lengths.tsv', sep='\t')
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Related Issues (20)
- Remove parameter --gsea_run HOT 1
- URGENT: pin nf-validation version HOT 2
- Dev version: On parameters website list parameter gene_sets_files in section GSEA HOT 1
- Name of blocking variable not correctly recognized HOT 7
- Continuous covariates HOT 6
- Please pin the version of the nf-validation plugin! HOT 1
- Error with samplesheet.csv with two column headers that have prefix in common HOT 8
- release differentialabundance HOT 1
- Process `NFCORE_DIFFERENTIALABUNDANCE:DIFFERENTIALABUNDANCE:GTF_TO_TABLE (gencode)` terminated with an error exit status (125) HOT 4
- Error in TABULAR_TO_GSEA_CHIP HOT 1
- GSEA html reports have broken links to png and TSV files HOT 1
- Failed to publish file => double forward slashes
- Auto-format sample names HOT 2
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- Missing colour and hover labels in interactive report volcano plot HOT 4
- Normalized/Raw data mishap on the report HOT 1
- Provide a parameter to disable rmarkdown report creation in the differential abundance pipeline HOT 2
- Requests: Enhancements to DESeq2 csv outputs and PDF outputs
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