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/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/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 Luo