Ask away!
I ran wf-transcriptomes on hpc cluster as follows -
`module load nextflow
export NXF_SINGULARITY_CACHEDIR=/data/$USER/nxf_singularity_cache;
export SINGULARITY_CACHEDIR=/data/$USER/.singularity;
export TMPDIR=/lscratch/$SLURM_JOB_ID
cp ${NXF_CONFIG_EPI2ME:-none} .
fastq_directory="/data/CDSL_LTG/DirectRNAseq/fastq_data_wf/"
#fastq_directory="/data/CDSL_LTG/DirectRNAseq/sam_files/"
gtf_file="/data/singha30/STAR.Genome/gencodeV43/gencode.v43.annotation.gtf"
genome_file="/data/singha30/STAR.Genome/hg38.fa"
sample_file="sample_sheet_symlinked.csv"
output_location="/data/CDSL_LTG/DirectRNAseq/EPI2ME"
nextflow run epi2me-labs/wf-transcriptomes
-profile biowulflocal
-resume
--direct_rna
--threads 10
--fastq $fastq_directory
--minimap2_index_opts '-k 14'
--ref_annotation $gtf_file
--ref_genome $genome_file
--out_dir $output_location
--sample_sheet $sample_file
#--sample "C33A_DirectRNA004" `
I didn't ran DE analysis. The run is complete and successful.
My question -> should there be an output file containing the aggregated and merged transcripts from across all the samples (38) that I analyzed. There is a separate merged gtf file for each sample, but should there be a final assembled transcriptome and gtf/gff file with aggregated information from across all samples that I can use for downstream analysis. I would appreciate the clarification or help.
Ask away!
I ran wf-transcriptomes on hpc cluster as follows -
`module load nextflow
export NXF_SINGULARITY_CACHEDIR=/data/$USER/nxf_singularity_cache;
export SINGULARITY_CACHEDIR=/data/$USER/.singularity;
export TMPDIR=/lscratch/$SLURM_JOB_ID
cp ${NXF_CONFIG_EPI2ME:-none} .
fastq_directory="/data/CDSL_LTG/DirectRNAseq/fastq_data_wf/"
#fastq_directory="/data/CDSL_LTG/DirectRNAseq/sam_files/"
gtf_file="/data/singha30/STAR.Genome/gencodeV43/gencode.v43.annotation.gtf"
genome_file="/data/singha30/STAR.Genome/hg38.fa"
sample_file="sample_sheet_symlinked.csv"
output_location="/data/CDSL_LTG/DirectRNAseq/EPI2ME"
nextflow run epi2me-labs/wf-transcriptomes
-profile biowulflocal
-resume
--direct_rna
--threads 10
--fastq $fastq_directory
--minimap2_index_opts '-k 14'
--ref_annotation $gtf_file
--ref_genome $genome_file
--out_dir $output_location
--sample_sheet $sample_file
#--sample "C33A_DirectRNA004" `
I didn't ran DE analysis. The run is complete and successful.
My question -> should there be an output file containing the aggregated and merged transcripts from across all the samples (38) that I analyzed. There is a separate merged gtf file for each sample, but should there be a final assembled transcriptome and gtf/gff file with aggregated information from across all samples that I can use for downstream analysis. I would appreciate the clarification or help.