rnaseq issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues2021-07-22T10:41:35-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/20Setting singularity to PWD doesnt work in the /work directory.2021-07-22T10:41:35-05:00Jeremy MathewsSetting singularity to PWD doesnt work in the /work directory.Must change nextflow.config to set the singularity directory.Must change nextflow.config to set the singularity directory.https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/19Update Astrocyte instructions2020-01-07T11:33:51-06:00Venkat MalladiUpdate Astrocyte instructions`One or more input paired-end FASTQ files from a RNASeq experiment and a design file with the link between the same name and the sample group``One or more input paired-end FASTQ files from a RNASeq experiment and a design file with the link between the same name and the sample group`Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/18Add Error ignore Stratagy2019-08-28T09:32:48-05:00Jeremy MathewsAdd Error ignore StratagyError Strategy was removed when testing. Add back into pipeline.Error Strategy was removed when testing. Add back into pipeline.Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/17Statanal Fail on single replicate2021-04-13T12:31:12-05:00Jeremy MathewsStatanal Fail on single replicateSkip statanal if # of samples is less than 2Skip statanal if # of samples is less than 2Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/16CheckDesignFile process2019-07-08T21:20:43-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduCheckDesignFile processnextflow.config sets all process to run on '128GB,256GB,256GBv1' nodes
```
process.queue='128GB,256GB,256GBv1'
```
that means that even the checkdesignfile process needs to wait on a high power process
you can make checkdesignfile bypas...nextflow.config sets all process to run on '128GB,256GB,256GBv1' nodes
```
process.queue='128GB,256GB,256GBv1'
```
that means that even the checkdesignfile process needs to wait on a high power process
you can make checkdesignfile bypass that to run on a super by:
```
process checkdesignfile {
queue 'super'
...
```Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/15Check file inputs2019-07-08T21:20:43-05:00Jeremy MathewsCheck file inputscheck for ".fq" or ".fastq" and gzip files to ".gz" formatcheck for ".fq" or ".fastq" and gzip files to ".gz" formatJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/14Fix CI2019-06-11T16:36:00-05:00Jeremy MathewsFix CIFix CI to remove bugs and run through checksFix CI to remove bugs and run through checksJeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/13An error in 'trimgalore.sh'2019-05-02T14:54:34-05:00Jeon LeeAn error in 'trimgalore.sh'Hi,
An user, skim17, reported an error generated during the 'trim' step such as [Process `trim (3)` terminated with an error exit status (1)]. After looking at the relevant scripts, we suspect that the error came from some lines in 'trim...Hi,
An user, skim17, reported an error generated during the 'trim' step such as [Process `trim (3)` terminated with an error exit status (1)]. After looking at the relevant scripts, we suspect that the error came from some lines in 'trimgalore.sh' below:
r1base="${fq1%.fastq*}"
r2base="${fq2%.fastq*}"
source /etc/profile.d/modules.sh
module load trimgalore/0.4.1 cutadapt/1.9.1
if [ -s $fq2 ]
then
trim_galore --paired -q 25 --illumina --gzip --length 35 ${fq1} ${fq2}
mv ${r1base}_val_1.fq.gz ${pair_id}.trim.R1.fastq.gz
mv ${r2base}_val_2.fq.gz ${pair_id}.trim.R2.fastq.gz
else
trim_galore -q 25 --illumina --gzip --length 35 ${fq1}
mv ${r1base}_trimmed.fq.gz ${pair_id}.trim.R1.fastq.gz
cp ${pair_id}.trim.R1.fastq.gz ${pair_id}.trim.R2.fastq.gz
fi
because the user's fastq file names are in a format of 'SampleID_ReplicateNumber_ReadNumber.fq.gz', e.g. 'ff_Cre_1_1.fq.gz'. In this case 'r1base' and 'r2base' are invalid.https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/12Fix dea.R2019-04-29T10:57:45-05:00Jonathan GesellFix dea.RCorrect link to corrected dea.R scriptCorrect link to corrected dea.R scriptJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/11Statanal fail at heatmaps2019-04-26T23:12:43-05:00Holly RuessStatanal fail at heatmapsThe dea.R script fails at the heatmap steps. This is caused by either the columnsums or rowsums of the zscore equals zeroThe dea.R script fails at the heatmap steps. This is caused by either the columnsums or rowsums of the zscore equals zeroJonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/10workflow/process_scripts empty after cloning2018-11-02T17:42:27-05:00Holly Ruessworkflow/process_scripts empty after cloningused git clone command to clone RNAseq pipeline. Process_scripts folder is empty and checked on git and noticed that the commit failed.used git clone command to clone RNAseq pipeline. Process_scripts folder is empty and checked on git and noticed that the commit failed.Brandi CantarelBrandi Cantarelhttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/9DEA Skip2018-05-16T16:04:11-05:00Jonathan GesellDEA SkipThere is an error in the main.nf when it checks for dea=skip, meaning that it will always run the DEA process.There is an error in the main.nf when it checks for dea=skip, meaning that it will always run the DEA process.Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/8Update of RNASeq documentation and check_designfile.pl2018-05-16T10:05:21-05:00Spencer BarnesUpdate of RNASeq documentation and check_designfile.pl1. The explanation of the design file should be updated to clarify that in addition to sampleIDs not starting with numbers, they should also not contain characters such as "." and "_".
2. check_designfile.pl should be updated to check...1. The explanation of the design file should be updated to clarify that in addition to sampleIDs not starting with numbers, they should also not contain characters such as "." and "_".
2. check_designfile.pl should be updated to check for this and end the run immediately if these characters are found. Currently, all steps in pipeline will complete successfully until the "statanal" step is reached where it will then fail.https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/7Vizapp shiny option: Implement Bookmarking for saving sessions on shiny app.2018-04-17T16:02:20-05:00Min KimVizapp shiny option: Implement Bookmarking for saving sessions on shiny app.Implement bookmarking option https://shiny.rstudio.com/articles/bookmarking-state.html to save states on shiny app.Implement bookmarking option https://shiny.rstudio.com/articles/bookmarking-state.html to save states on shiny app.Danni LuoDanni Luohttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/6Genearte Signal Tracks2018-04-10T16:27:31-05:00Venkat MalladiGenearte Signal TracksGenerate Signal Tracks for Vizualization in Browser. (Can use deeptools)Generate Signal Tracks for Vizualization in Browser. (Can use deeptools)https://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/5Deeptools QC metics between samples2018-04-10T16:26:53-05:00Venkat MalladiDeeptools QC metics between samplesPlot Spearman Correlation between samples using Deeptools:
http://deeptools.readthedocs.io/en/latest/content/tools/plotCorrelation.htmlPlot Spearman Correlation between samples using Deeptools:
http://deeptools.readthedocs.io/en/latest/content/tools/plotCorrelation.htmlDanni LuoDanni Luohttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/4RNASeq Pathway Analysis Mouse support2018-04-10T16:21:07-05:00Venkat MalladiRNASeq Pathway Analysis Mouse supportCurrently the workflow doesn't work for mouse genesets -- probably an error in the qusage code in dea.R -- see geneset files in:
/project/shared/bicf_workflow_ref/GRCm38/gsea_gmt/Currently the workflow doesn't work for mouse genesets -- probably an error in the qusage code in dea.R -- see geneset files in:
/project/shared/bicf_workflow_ref/GRCm38/gsea_gmt/Danni LuoDanni Luohttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/3Update RNASeq Shiny Code2018-11-19T11:11:41-06:00Venkat MalladiUpdate RNASeq Shiny Code1) Add ability to download QuSAGE output table (pathway analysis)
2) Heatmap with no sample clustering1) Add ability to download QuSAGE output table (pathway analysis)
2) Heatmap with no sample clusteringDanni LuoDanni Luohttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/2RNASeq New Isoform Detection2021-04-13T12:31:57-05:00Brandi CantarelRNASeq New Isoform DetectionDevelop a workflow for the detection of Exon Skipping, Intron Inclusion (exon extension).Develop a workflow for the detection of Exon Skipping, Intron Inclusion (exon extension).Danni LuoDanni Luohttps://git.biohpc.swmed.edu/BICF/Astrocyte/rnaseq/-/issues/1star broken2018-04-30T09:57:41-05:00Spencer Barnesstar brokenPipeline fails when running with STAR alignment option. Confirmed on two separate runs with different datasets.Pipeline fails when running with STAR alignment option. Confirmed on two separate runs with different datasets.