BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2019-05-02T14:54:34-05:00https://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/cellranger_mkfastq/-/issues/19Move params out of main.nf2019-04-26T15:47:15-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove params out of main.nfGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/6Trimming Comparison2020-12-29T17:29:23-06:00Jonathan GesellTrimming ComparisonTesting the most efficient and effective trimmer.Testing the most efficient and effective trimmer.https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/39Optimizations2020-06-23T15:51:07-05:00Jonathan GesellOptimizationsGeneral speed-ups and optimization of pipeline branches.General speed-ups and optimization of pipeline branches.3.0.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/16Move params out of main.nf2020-04-13T11:37:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduMove params out of main.nfWait for astroycte update to handle custom configsWait for astroycte update to handle custom configshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/32Memory2020-06-23T15:56:18-05:00Venkat MalladiMemoryChange Python max mem to maybe 3/4 (test), for samtools sortChange Python max mem to maybe 3/4 (test), for samtools sort3.0.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/10Add ability to count additional features2020-06-21T13:57:51-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd ability to count additional featureshttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customhttps://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/feature-bc-analysis
Ab
CRISPR
customPendingGervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://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/atacseq_analysis/-/issues/1map_reads failure case2020-06-23T16:03:04-05:00Spencer Barnesmap_reads failure caseWhen map_reads.py fails to find the input files, empty bam files are still created. This should probably give a non zero exit status instead.When map_reads.py fails to find the input files, empty bam files are still created. This should probably give a non zero exit status instead.Version 2.1.0Holly RuessHolly Ruesshttps://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/chipseq_analysis/-/issues/14Add in peak call with SPP and IDR2020-06-23T15:50:40-05:00Venkat MalladiAdd in peak call with SPP and IDR2.0.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/9Add in blacklist2020-06-23T15:50:34-05:00Venkat MalladiAdd in blacklistAdd blacklist support for mm9,mm10,hg19,hg38Add blacklist support for mm9,mm10,hg19,hg382.0.0Venkat MalladiVenkat Malladi