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Hi Jianhong,
Thank you again so much for creating ATACseqQC!
To get the report of all the QC metrics with bamQC, it looks like I should use:
**bamQC(bamFile, outPath = NULL)**
To get the bam…
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I downloaded the source code using the link from [Pypi](https://github.com/mhammell-laboratory/bamqc/archive/0.6.4.tar.gz), and tried to install using the instructions in [doc/INSTALL](https://github.…
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## Unused arguments
Many variables in this function are never used (I might be missing some perl scoping magic):
https://github.com/oicr-gsi/bamqc/blob/a3964603efc86334e3345d30c331c9aacab256b2/lib/G…
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Hi Jianhong,
Besides the reads with low alignment scores, the reads derived from mitochondrial DNA and the PCR/optical duplicates, are there any other filters applied by bamQC?
What are the parame…
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> `pepatac/tools/bamQC.py -i pepatac_test/nn1/aligned_mm10/nn1_sort.bam -c 1 -o pepatac_test/nn1/QC_mm10/nn1_bamQC.tsv` (56981)
Traceback (most recent call last):
File "pepatac/tools/bamQC.py", …
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I installed version 0.6.4 onto a server (genomics), and set the --prefix to ~/software/BAMqc/inst. Although the BAMqc executable was placed correctly into the bin folder, it can't be run from the bin …
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Help documentation for BamQC modules
pdp10 updated
8 years ago
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Hi, when doing a test run with the test1 files provided the script is running until the test1_bamQC.tsv should be created. At this point I am getting an error message:
NameError: name '_LOGGER' is…
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Hello,
I have a question about what the insert size plot is calculating exactly. I ask because I get the same profile, but different numbers, with Picard [CollectInsertSizeMetrics](https://broadinsti…
ewels updated
8 years ago
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The parsed CIGAR string is reversed if it is on the - strand:
https://github.com/oicr-gsi/bamqc/blob/a3964603efc86334e3345d30c331c9aacab256b2/lib/GSI/bamqc.pm#L1900
I assume the `$strand` variable…