Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-3772

Run NEXTFLOW on contigs that are NOT SL4 or SL5

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Minor
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          Description

          GOAL:
          To set up and run an nf-core/rna-seq pipeline to align our RNA-Seq sequences against the de novo created contigs (Trinity, Spades).

          Next flow requires a GTF and a bed file along with the contigs. There are various ways to generate these and it is possible issues will arise from these files.

          Otherwise, we can follow Molly's protocol:
          https://docs.google.com/document/d/1ig9ET-ykXF5nAX3P487cXWmZDGUlQpcwrvFXpbyP5vw/edit?usp=sharing

            Attachments

              Issue Links

              blocks

              Task - A task that needs to be done. IGBF-3817 Create a method to compare NextFlow gene expression results

              • Major - Major loss of function.
              • To-Do

                Activity

                Ascending order - Click to sort in descending order
                10 older comments
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                Rob needs to review that all 4 runs appear complete.

                Will check for proper bam sizes, bai, and bedgraphs, etc.
                And that the salmon table exists.

                Show
                robofjoy Robert Reid added a comment - Rob needs to review that all 4 runs appear complete. Will check for proper bam sizes, bai, and bedgraphs, etc. And that the salmon table exists.
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                In Mal, Hei, Nag, Tam, there are the full compliment of bam files and bai index files.
                And the sizes appear correct.

                For tsv salmon counts, it looks as though only Heinz has the tsv file of counts, the other 3 runs do not.
                Something is amiss !

                In mal, there is an error along the nextflow path:

                Command executed:

                inner_distance.py \
                -i M.25C.0hr.U.1.sorted.bam \
                -r blat-mal.bed \
                -o M.25C.0hr.U.1 \
                \
                > stdout.txt
                head -n 2 stdout.txt > M.25C.0hr.U.1.inner_distance_mean.txt

                cat <<-END_VERSIONS > versions.yml
                "NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE":
                rseqc: $(inner_distance.py --version | sed -e "s/inner_distance.py //g")
                END_VERSIONS

                And in Tam, there is a totally different error, it gets further along before error occurs.

                These are nasty in that they do not crash the pipeline but let it continue rolling along.
                We need to back up a few steps and rerun Mal, Tam and Nag.

                Show
                robofjoy Robert Reid added a comment - In Mal, Hei, Nag, Tam, there are the full compliment of bam files and bai index files. And the sizes appear correct. For tsv salmon counts, it looks as though only Heinz has the tsv file of counts, the other 3 runs do not. Something is amiss ! In mal, there is an error along the nextflow path: Command executed: inner_distance.py \ -i M.25C.0hr.U.1.sorted.bam \ -r blat-mal.bed \ -o M.25C.0hr.U.1 \ \ > stdout.txt head -n 2 stdout.txt > M.25C.0hr.U.1.inner_distance_mean.txt cat <<-END_VERSIONS > versions.yml "NFCORE_RNASEQ:RNASEQ:BAM_RSEQC:RSEQC_INNERDISTANCE": rseqc: $(inner_distance.py --version | sed -e "s/inner_distance.py //g") END_VERSIONS And in Tam, there is a totally different error, it gets further along before error occurs. These are nasty in that they do not crash the pipeline but let it continue rolling along. We need to back up a few steps and rerun Mal, Tam and Nag.
                Hide
                Permalink
                bbendick Brandon Bendickson added a comment -

                Results are found in /projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh
                for Nag, Tam, and Mal

                Show
                bbendick Brandon Bendickson added a comment - Results are found in /projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh for Nag, Tam, and Mal
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                Looks like we now have the proper tsv salmon count files needed for the next step.

                Lots of them.
                rreid2@str-i2:/projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh$ ls Tam-run-2/results-3.14.0/star_salmon/*tsv
                Tam-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_length_scaled.tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_counts.tsv
                Tam-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_scaled.tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_lengths.tsv
                Tam-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts.tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_tpm.tsv
                Tam-run-2/results-3.14.0/star_salmon/salmon.merged.gene_lengths.tsv Tam-run-2/results-3.14.0/star_salmon/tx2gene.tsv
                Tam-run-2/results-3.14.0/star_salmon/salmon.merged.gene_tpm.tsv
                rreid2@str-i2:/projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh$ ls Mal-run-2/results-3.14.0/star_salmon/*tsv
                Mal-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_length_scaled.tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_counts.tsv
                Mal-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_scaled.tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_lengths.tsv
                Mal-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts.tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_tpm.tsv
                Mal-run-2/results-3.14.0/star_salmon/salmon.merged.gene_lengths.tsv Mal-run-2/results-3.14.0/star_salmon/tx2gene.tsv
                Mal-run-2/results-3.14.0/star_salmon/salmon.merged.gene_tpm.tsv
                rreid2@str-i2:/projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh$ ls Nag-run-2/results-3.14.0/star_salmon/*tsv
                Nag-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_length_scaled.tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_counts.tsv
                Nag-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_scaled.tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_lengths.tsv
                Nag-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts.tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_tpm.tsv
                Nag-run-2/results-3.14.0/star_salmon/salmon.merged.gene_lengths.tsv Nag-run-2/results-3.14.0/star_salmon/tx2gene.tsv
                Nag-run-2/results-3.14.0/star_salmon/salmon.merged.gene_tpm.tsv

                Show
                robofjoy Robert Reid added a comment - Looks like we now have the proper tsv salmon count files needed for the next step. Lots of them. rreid2@str-i2:/projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh$ ls Tam-run-2/results-3.14.0/star_salmon/*tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_length_scaled.tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_counts.tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_scaled.tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_lengths.tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts.tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_tpm.tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.gene_lengths.tsv Tam-run-2/results-3.14.0/star_salmon/tx2gene.tsv Tam-run-2/results-3.14.0/star_salmon/salmon.merged.gene_tpm.tsv rreid2@str-i2:/projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh$ ls Mal-run-2/results-3.14.0/star_salmon/*tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_length_scaled.tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_counts.tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_scaled.tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_lengths.tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts.tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_tpm.tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.gene_lengths.tsv Mal-run-2/results-3.14.0/star_salmon/tx2gene.tsv Mal-run-2/results-3.14.0/star_salmon/salmon.merged.gene_tpm.tsv rreid2@str-i2:/projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh$ ls Nag-run-2/results-3.14.0/star_salmon/*tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_length_scaled.tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_counts.tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts_scaled.tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_lengths.tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.gene_counts.tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.transcript_tpm.tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.gene_lengths.tsv Nag-run-2/results-3.14.0/star_salmon/tx2gene.tsv Nag-run-2/results-3.14.0/star_salmon/salmon.merged.gene_tpm.tsv
                Hide
                Permalink
                robofjoy Robert Reid added a comment -

                And all the bam files exist:

                To check:
                /projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh$ ls -lrt Tam-run-2/results-3.14.0/star_salmon/*bam

                There are some size discrepancies across the bam files, the smallest being 800MB and the largest 5GB. But no idea if that is anything to be concerned about.

                Next phase: Create 1 large salmon counts file using the results from these 4 salmon files. That means new ticket!

                Show
                robofjoy Robert Reid added a comment - And all the bam files exist: To check: /projects/tomato_genome/fnb/dataprocessing/brandon_work/NEXTFLOW/start_fresh$ ls -lrt Tam-run-2/results-3.14.0/star_salmon/*bam There are some size discrepancies across the bam files, the smallest being 800MB and the largest 5GB. But no idea if that is anything to be concerned about. Next phase: Create 1 large salmon counts file using the results from these 4 salmon files. That means new ticket!

                  People

                  • Assignee:
                    robofjoy Robert Reid
                    Reporter:
                    robofjoy Robert Reid
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: