atacseq_analysis issueshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/issues2020-01-02T14:26:27-06:00https://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/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/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 Ruess