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/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/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/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/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/21Fix concurrent runners2020-05-28T13:59:21-05:00Venkat MalladiFix concurrent runnersVenkat MalladiVenkat Malladihttps://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/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/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/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/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/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/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/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 Ruess