BICF issueshttps://git.biohpc.swmed.edu/groups/BICF/-/issues2020-03-24T14:23:39-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/28Add percent of reads - mitochondria2020-03-24T14:23:39-05:00Holly RuessAdd percent of reads - mitochondriaDo this at the filter bam file step; may need to divide the filter into multiple parts to include this step. Add into multiQC report but don't set a cutoffDo this at the filter bam file step; may need to divide the filter into multiple parts to include this step. Add into multiQC report but don't set a cutoffVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/28Comparison Script2020-04-25T19:02:01-05:00Venkat MalladiComparison ScriptComparison between current database and updates.Comparison between current database and updates.Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/sra_pipeline/-/issues/28Fix README2020-11-25T12:08:39-06:00Jeremy MathewsFix READMEFix readme instructions for running to clone sra pipeline instead of metagenome analysis pipeline.
Update module versions (singularity and nextflow) in module load command.Fix readme instructions for running to clone sra pipeline instead of metagenome analysis pipeline.
Update module versions (singularity and nextflow) in module load command.Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/31Add human mouse mix reference v3.1.02019-07-31T14:35:46-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd human mouse mix reference v3.1.0Changes needed:
* [x] astrocyte_pkg.yml
* code has to be: GRCh38-and-mm10-3.1.0
* text should be 'Human GRCh38 + Mouse GRCm38 (mm10) release 93'
* put it directly above the two other human mouse mixes
* *NOTE: please fix mm19 to mm10*
...Changes needed:
* [x] astrocyte_pkg.yml
* code has to be: GRCh38-and-mm10-3.1.0
* text should be 'Human GRCh38 + Mouse GRCm38 (mm10) release 93'
* put it directly above the two other human mouse mixes
* *NOTE: please fix mm19 to mm10*
* [x] biohpc.config
* In params:genomes: add the code from astrocyte_pkg.yml translation to physical location than Paniz will hopefully be making for us (see slack message)
* [x] README.md & index.mdv1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/29add plotProfile2020-03-15T12:57:07-05:00Holly Ruessadd plotProfileAdd plotProfile for each sampleAdd plotProfile for each sample1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/29Fix CountDesign2019-08-05T11:16:22-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduFix CountDesign1 bcl.tar.gz
multiple samples
= only last sample lists fastq's and it is the first sample's fastq's
see file attached:
[Cellranger_Count_Design.csv](/uploads/a4091f3f71e24fc25068c99a19181d2c/Cellranger_Count_Design.csv)1 bcl.tar.gz
multiple samples
= only last sample lists fastq's and it is the first sample's fastq's
see file attached:
[Cellranger_Count_Design.csv](/uploads/a4091f3f71e24fc25068c99a19181d2c/Cellranger_Count_Design.csv)v1.3.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/29Add FRiP score2020-05-13T09:30:50-05:00Holly RuessAdd FRiP score# total reads
total_reads=$(samtools view -c ${sample}.bam)
# reads in peaks
reads_in_peaks=$(bedtools sort -i ${sample}_peaks.narrowPeak \
| bedtools merge -i stdin | bedtools intersect -u -nonamecheck \
-a ${sample}.bam -b stdin -...# total reads
total_reads=$(samtools view -c ${sample}.bam)
# reads in peaks
reads_in_peaks=$(bedtools sort -i ${sample}_peaks.narrowPeak \
| bedtools merge -i stdin | bedtools intersect -u -nonamecheck \
-a ${sample}.bam -b stdin -ubam | samtools view -c)
# FRiP score
FRiP=$(awk "BEGIN {print "${reads_in_peaks}"/"${total_reads}"}")
Do this step after calling peaks; add in multiQC report
Colored cutoff:
The fraction of reads in called peak regions (FRiP score) should be >0.3, though values greater than 0.2 are acceptable. For EN-TEx tissues (ENCODE GTEx tissue sample), FRiP scores will not be enforced as QC metric. TSS enrichment remains in place as a key signal to noise measure.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/29Gender to sex2020-07-01T20:02:32-05:00Venkat MalladiGender to sexVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/32Add more artifacts to CI2019-07-31T14:35:47-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd more artifacts to CI* web_summary.html
* multiqc_report.html* web_summary.html
* multiqc_report.htmlv1.2.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/30xcor.py, --random-source fails if file is too small2020-03-15T12:56:59-05:00Holly Ruessxcor.py, --random-source fails if file is too smallpossible fix:
# Make the file bigger so that --random-source can work
tags2 = 'cat.tagAlign.gz'
out, err = utils.run_pipe([
"zcat %s %s %s" %
(tag, tag, tag)
], outfile=tags2)
steps = [
'zcat %s' ...possible fix:
# Make the file bigger so that --random-source can work
tags2 = 'cat.tagAlign.gz'
out, err = utils.run_pipe([
"zcat %s %s %s" %
(tag, tag, tag)
], outfile=tags2)
steps = [
'zcat %s' % (tag),
'grep -v "chrM"',
'shuf -n %d --random-source=%s' % (NREADS, tags2)]1.1.0Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_mkfastq/-/issues/30Add multiqc output to CI artifacts2019-08-14T23:31:42-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd multiqc output to CI artifactsv1.3.1Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/30TSS enrichment score2020-05-28T20:56:04-05:00Holly RuessTSS enrichment scoreSee ATAqc for code in python for this.See ATAqc for code in python for this.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/KCE/kce_etl/-/issues/30Update cancer gene2020-10-19T17:33:19-05:00Venkat MalladiUpdate cancer geneUpdate cancer gene
If IHC says gene (IHC) or gene (Sequencing)Update cancer gene
If IHC says gene (IHC) or gene (Sequencing)Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/33Exclude changes in *.md for CI2019-07-31T23:55:49-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduExclude changes in *.md for CIexcept:
changes:
- "*.md"except:
changes:
- "*.md"Jeremy MathewsJeremy Mathewshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/50Generate Raw RDS file2020-08-14T14:01:39-05:00Venkat MalladiGenerate Raw RDS fileProvide Raw RDS file per sample (Seurat object)Provide Raw RDS file per sample (Seurat object)2.2.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/55Add cellranger 5.0.02020-11-20T09:57:21-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd cellranger 5.0.03.0.0Spencer BarnesSpencer Barneshttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/56Add 5GEXPE/SE as library options2020-11-20T12:13:22-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduAdd 5GEXPE/SE as library optionsAuto 5GEX misidentify 5GEXSE as PE when sequencing strategy not customizedAuto 5GEX misidentify 5GEXSE as PE when sequencing strategy not customized3.0.0Gervaise Henrygervaise.henry@utsouthwestern.eduGervaise Henrygervaise.henry@utsouthwestern.eduhttps://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/545GEX QC data not present in multiqc report2020-11-04T10:06:00-06:00Gervaise Henrygervaise.henry@utsouthwestern.edu5GEX QC data not present in multiqc report# Summary
# Steps to reproduce
# Observed bug behavior
# Expected behavior
# Relevant logs and/or screenshots
# Potential fixes
/cc @ghenry# Summary
# Steps to reproduce
# Observed bug behavior
# Expected behavior
# Relevant logs and/or screenshots
# Potential fixes
/cc @ghenry3.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/cellranger_count/-/issues/48Update multiqc version/references report2020-11-03T12:29:40-06:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add pipeline zenodo references report
* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)3.0.0https://git.biohpc.swmed.edu/BICF/Astrocyte/chipseq_analysis/-/issues/31skip motif search and diff bind2019-03-12T14:07:41-05:00Holly Ruessskip motif search and diff bindWe don't need to run the analysis all the time. Allow for the skipping of these stepsWe don't need to run the analysis all the time. Allow for the skipping of these steps1.0.0Venkat MalladiVenkat Malladi