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SPEAQeasy currently relies on Bioc 3.13, where a [bug in the GenomeInfoDB package](https://github.com/Bioconductor/GenomeInfoDb/issues/30) results in the `BuildAnnotationObjects` process failing [here…
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The start coordinate of junctions seem to be off by 2 (i.e. using start+2 seems to produce the "correct" coordinate). Junction counts are generated by `regtools` in a BED file which is then parsed by …
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Reasons:
* reprocess with the latest HISAT2
* fix rse_jx data properly
* test the pipeline on unstranded (polyA) data
FASTQ files located in `/dcl01/ajaffe/data/Nina/BrainSeq_PhaseI/DLPFC_PolyA/…
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It seems the primary alignments BAM files are only created because `regtools junctions extract` requires a BAM index, due to the `-r` option, as seen here: https://github.com/griffithlab/regtools/blo…
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This can be done in different ways.
* Plot the top principal components against each other and color them by some covariates we have.
* Plot top PCS one at a time using boxplots or scatterplots a…
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We will plan to support managing software dependencies using docker. This will require the creation of some new docker images. In particular, we'll likely need to produce an image for the trimming and…
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At JHPCE, we are using R 4.0 via the module `conda_R/4.0`. Eventually, we'll want SPEAQeasy to use R 4.0 regardless of platform (rather than the current 3.6.1 for non-JHPCE users). In addition, we sho…
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Write a script that can download the example data. The example DNA genotype data might live in this repo if it's tiny (depends on #2). The FASTQ data should ideally already be publicly available given…
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I try to install the SPEAQeasy in my local computer but when I run "install_software.sh" it crash in some part.
Do you have some idea for fix it?
The error message is it:
Loading required packa…
ehatl updated
3 years ago
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In the "second half", we collect metrics from trimming, alignment, and more, which are compiled into a data frame. Right now, we perform FastQC, and results determine whether trimming is performed. Ho…