atacseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues2020-07-29T07:44:38-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/43map reads fails to make bam files for long reads2020-07-29T07:44:38-05:00Venkat Malladimap reads fails to make bam files for long readshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/blob/dev/workflow/scripts/map_reads.py#L239
Doesn't make sam files or bam fileshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/blob/dev/workflow/scripts/map_reads.py#L239
Doesn't make sam files or bam filesVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/42Update to astrocyte 0.3.12020-07-01T14:35:53-05:00Venkat MalladiUpdate to astrocyte 0.3.1Version 2.1.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/41Update multiqc version/references report2020-07-01T14:36:11-05:00Gervaise Henrygervaise.henry@utsouthwestern.eduUpdate multiqc version/references report* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)* Add astrocyte version to version report (if param.astrocyte=true)
* Add astrocyte reference to reference report (if param.astrocyte=true)Version 2.1.0https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/40Astrocyte fixes2020-06-21T05:07:11-05:00Venkat MalladiAstrocyte fixesUpdate astrocyte yaml to be more informative
Update astrocyte to get the version of the reference genomeUpdate astrocyte yaml to be more informative
Update astrocyte to get the version of the reference genomeVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/39Tests for astrocyte2020-06-18T08:32:27-05:00Venkat MalladiTests for astrocyteVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/38Add license2020-05-07T15:53:13-05:00Venkat MalladiAdd licenseVersion 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/37Fix runners and sigbus error2020-05-08T10:01:55-05:00Venkat MalladiFix runners and sigbus errorVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/36update version of nextflow2020-06-23T16:02:27-05:00Holly Ruessupdate version of nextflowupdate nextflow/0.31.0 to nextflow/19.09.0update nextflow/0.31.0 to nextflow/19.09.0Version 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/35Change to 256 only if job fails2020-06-23T16:02:34-05:00Holly RuessChange to 256 only if job failsMay need to incorporate maxErrors and maxRetries into processesMay need to incorporate maxErrors and maxRetries into processesVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/34Diff Peak analysis2020-06-23T16:02:40-05:00Holly RuessDiff Peak analysisVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/33Motif search in peaks2020-06-23T16:02:46-05:00Holly RuessMotif search in peaksVersion 2.1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/32Annotate peaks2020-06-11T16:18:58-05:00Holly RuessAnnotate peaksVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/31Blacklist of regions2020-06-09T14:55:50-05:00Holly RuessBlacklist of regionsAdd a blacklist of regions to ignore for each genomeAdd a blacklist of regions to ignore for each genomeVersion 2.0Holly RuessHolly Ruesshttps://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/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/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/Astrocyte/atacseq_analysis/-/issues/27Add fragment size distribution2020-06-09T09:15:49-05:00Holly RuessAdd fragment size distributionMake a graphic of fragment size distributionMake a graphic of fragment size distributionVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/26Generate MultiQC report2020-02-25T07:45:39-06:00Holly RuessGenerate MultiQC reportVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/25Fix BioHPC config2020-01-07T09:38:50-06:00Holly RuessFix BioHPC configWARN: The config file defines settings for an unknown process: tssEnrich
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$checkDesignFile = <value>` with a process selector
[warm up] executor > loc...WARN: The config file defines settings for an unknown process: tssEnrich
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$checkDesignFile = <value>` with a process selector
[warm up] executor > local
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$trimReads = <value>` with a process selector
[warm up] executor > slurm
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$alignReads = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$filterReads = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$experimentQC = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$convertReads = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$crossReads = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$defineExpDesignFiles = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$poolAndPsuedoReads = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$callPeaksMACS = <value>` with a process selector
WARN: Process configuration syntax $processName has been deprecated -- Replace `process.$consensusPeaks = <value>` with a process selector
Also remove GRCh37Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/24fix consensus peaks2020-01-07T09:35:33-06:00Holly Ruessfix consensus peaksVersion 2.0Holly RuessHolly Ruess