atacseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues2020-06-23T16:03:04-05:00https://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/atacseq_analysis/-/issues/2deeptools version 3 error2020-01-02T14:27:29-06:00Spencer Barnesdeeptools version 3 errorWhen calculating signal using bamCoverage, deeptools version 3 does not recognize output of filter_reads step as bam files. Deeptools version 2.5.* does work currently.When calculating signal using bamCoverage, deeptools version 3 does not recognize output of filter_reads step as bam files. Deeptools version 2.5.* does work currently.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/3mitochondrial chromosome reads2020-01-02T14:26:27-06:00Spencer Barnesmitochondrial chromosome readsRe-write script to remove mitochondrial reads as an option. We should also get the percentage of mitochondrial reads in all reads.Re-write script to remove mitochondrial reads as an option. We should also get the percentage of mitochondrial reads in all reads.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/4pool and pseudoreplicate2020-01-02T14:24:34-06:00Spencer Barnespool and pseudoreplicatepool_and_pseudoreplicate.py script creates temporary working files which interfere with one another when running various instances in the same directory.pool_and_pseudoreplicate.py script creates temporary working files which interfere with one another when running various instances in the same directory.Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/5Re-direct output2020-01-02T14:24:08-06:00Holly RuessRe-direct outputAdd an option to name the output folderAdd an option to name the output folderVersion 2.0Holly RuessHolly Ruesshttps://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/atacseq_analysis/-/issues/7Shift is incorrect for ATAC-seq2020-01-06T13:57:44-06:00Venkat MalladiShift is incorrect for ATAC-seqShift should be switchted in call_peaks_macs2.py
`--shift 73 --extsize %s`
shift 37 and extsize 73Shift should be switchted in call_peaks_macs2.py
`--shift 73 --extsize %s`
shift 37 and extsize 73Version 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/8Make ATAC-seq pipeline generalizibe for Open Chromatin2019-12-03T10:26:25-06:00Venkat MalladiMake ATAC-seq pipeline generalizibe for Open ChromatinVersion 1.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/9Add in references and version used in script2020-05-28T13:58:53-05:00Venkat MalladiAdd in references and version used in scriptVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/10Update script to incorrpoarte chagnes from ChiP_seq pipeline2019-12-03T10:27:14-06:00Venkat MalladiUpdate script to incorrpoarte chagnes from ChiP_seq pipelineUpdate scripts to include changes to sample names and outputfolderUpdate scripts to include changes to sample names and outputfolderVersion 1.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/11Change output from png to pdf2020-01-02T14:23:29-06:00Holly RuessChange output from png to pdfAny graphic that is a *.png needs to be *.pdf
This is for better qualityAny graphic that is a *.png needs to be *.pdf
This is for better qualityVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/12Remove unnecessary columns from design file2019-12-04T08:53:16-06:00Holly RuessRemove unnecessary columns from design fileDesign file is the same as chip-seq. Some columns are never used, so we should just remove themDesign file is the same as chip-seq. Some columns are never used, so we should just remove themVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/13update check design file2019-12-09T13:27:55-06:00Holly Ruessupdate check design fileUpdate check design file and add seq lengthUpdate check design file and add seq lengthVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/14Fix Trim Reads2019-12-11T08:23:17-06:00Holly RuessFix Trim ReadsMake corrections to Trim ReadsMake corrections to Trim ReadsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/15Fix Filter Reads2019-12-18T08:03:54-06:00Holly RuessFix Filter ReadsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/16Fix Align Reads2019-12-16T17:14:34-06:00Holly RuessFix Align ReadsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/17Fix Experiment QC2019-12-20T10:28:15-06:00Holly RuessFix Experiment QCVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/18Fix Convert Reads2019-12-27T14:34:30-06:00Holly RuessFix Convert ReadsVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/19Fix cross correlation2020-01-03T08:47:05-06:00Holly RuessFix cross correlationVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/20Fix Pool and Pseudoreps2020-01-03T08:47:15-06:00Holly RuessFix Pool and PseudorepsVersion 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/21Fix concurrent runners2020-05-28T13:59:21-05:00Venkat MalladiFix concurrent runnersVenkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/22Make hg19 test2020-01-06T14:03:38-06:00Holly RuessMake hg19 testVersion 2.0Holly RuessHolly Ruesshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues/23Fix call peaks MACs2020-01-07T09:36:31-06:00Holly RuessFix call peaks MACsVersion 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 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/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/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/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/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/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/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/32Annotate peaks2020-06-11T16:18:58-05:00Holly RuessAnnotate peaksVersion 2.0Holly 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/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/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/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/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/38Add license2020-05-07T15:53:13-05:00Venkat MalladiAdd licenseVersion 2.0Venkat 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/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/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/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/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 Malladi