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epi2me-labs / wf-transcriptomes

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About gene and isoform count matrix #30

Closed wuy24 closed 9 months ago

wuy24 commented 10 months ago

Ask away!

I am using wf-transcriptomes workflow for analysis my ONT pilote transcriptome data which is from only 1cDNA library. After I run the following command, the result I got are the html report, transcriptome.fas and somt gtf and tsv files in _gffcompare folder. However, I wonder if there is any way that I can generate the quantification count matrix at gene level and isoform level. Thank you!

nextflow run epi2me-labs/wf-transcriptomes -profile singularity -c mynextflow.config --fastq sample.fastq.gz --ref_genome /mnt/ccrsf-ifx/RefGenomes/hg38_SEQC/hg38.fa --ref_annotation /mnt/ccrsf-ifx/RefGenomes/hg38/GTF/gencode.v41.primary_assembly.annotation.gtf --pychopper_opts '-k PCS111' --threads 32 --out_dir outdir -w workspace_dir

Best, Ying

sarahjeeeze commented 10 months ago

Hi, the count matrices are only created when using the differential gene expression option so the --de_analysis for this option a sample sheet is also required and you need 3 repeats per condition. If its of interest and use we could consider outputting the table you see in the isoforms table at the bottom of the report (not in de analysis mode) as a tsv file output file.

sarahjeeeze commented 9 months ago

Closing through lack of response.