Molly Davis added a comment - 18/Jan/23 11:41 AM - edited Update: I fixed the sample sheet so that strandedness is reverse. When running nextflow I come across this error for trimgalore: Command error: INFO: Converting SIF file to temporary sandbox... Path to Cutadapt set as: 'cutadapt' ( default ) Cutadapt seems to be working fine (tested command 'cutadapt --version') Cutadapt version: 3.4 Could not detect version of Python used by Cutadapt from the first line of Cutadapt (but found this : >>>#!/bin/sh<<<) Letting the (modified) Cutadapt deal with the Python version instead Parallel gzip (pigz) detected. Proceeding with multicore (de)compression using 4 cores No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores ( default ) Input file 'MP-MC-1_1.fastq.gz' seems to be completely empty. Consider respecifying! INFO: Cleaning up image... Work dir: /nobackup/tomato_genome/seedlingPollen/nfcore/work/15/4c200c1d0331cd19fc66b69eaad96b Question: are all fastq files double stranded or single stranded? Or is there a naming issue in the sample csv file? Next step : Instead of using symbolic links I will copy the fastq files to the following directory to see if it works with nextflow. I have had issues with symbolic links before with fastq files and copying the files instead seemed to fix the issue. Copy From : /projects/tomato_genome/rnaseq/mark-2022-pollengrainSeedling/00_fastq/ Copy To : /nobackup/tomato_genome/seedlingPollen/nfcore Issue: Do not have permission to copy fastq files. Fixed Issue: Dr. Robert Reid gave permission so I could copy files over.

Molly Davis added a comment - 18/Jan/23 3:36 PM - edited Nextflow Pipeline Ran Successfully! Directory: /nobackup/tomato_genome/seedlingPollen/nfcore Next steps: Rename sorted bam files and make scaled coverage graphs.

Molly Davis added a comment - 19/Jan/23 12:57 PM - edited Scaled coverage graphs have been made and are located: /nobackup/tomato_genome/seedlingPollen/nfcore/results/star_salmon Notes: I can move the coverage graphs to their own directory if you would like. Let me know! Multiqc Report: scp mdavi258@hpc.uncc.edu:/nobackup/tomato_genome/seedlingPollen/nfcore/results/multiqc/star_salmon/multiqc_report.html nfcore_multiqc_report.html nfcore_multiqc_report.html Notes: Seems there are no issues with strandedness. Next step : Pipeline, coverage graphs, and Multiqc report need to be reviewed. [~aloraine]

Ann Loraine added a comment - 28/Jan/23 1:06 PM Ran find junctions pipeline. Copied data to host with: scp -J aloraine@hop.renci.org -r junctions aloraine@lorainelab-quickload.scidas.org:/projects/igbquickload/lorainelab/www/main/htdocs/hotpollen/S_lycopersicum_Jun_2022/mark-2022-timeseries/.

Ann Loraine added a comment - 28/Jan/23 1:07 PM Added samples.csv file to repository. See: https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/seedlingPollen-samples.csv

Ann Loraine added a comment - 28/Jan/23 1:09 PM Got description of data set. See attached.

Ann Loraine added a comment - 29/Jan/23 1:22 PM Deployed data to quickload. Did not examine pattern of coverage graphs relative to other data sets. Added sample sheet to repositor: https://bitbucket.org/hotpollen/splicing-analysis/src/main/ExternalData/seedlingPollen_sample_sheet.xlsx