Counts

Output Directory: results/counts/

Rules

• alignment.smk

  • KallistoQuant

• diffexp.smk

  • DifferentialGeneExpression

  • DifferentialIsoformExpression

Introduction

Counting reads to genes is an important step in the analysis of RNA-seq data. The raw data from an RNA-seq experiment consists of millions of reads that are derived from the RNA molecules in the sample. In order to quantify gene expression, these reads must be mapped to the transcript from which they were derived, and the number of reads mapped to each transcript must be counted. This process, known as read counting, provides a measure of the abundance of each gene in each sample and can be used to identify differentially expressed genes and other interesting features of the data.

In RNA-Seq-Pop we map reads directly to the transcriptome with kallisto, a process termed ‘pseudoalignment’. This has the benefit of being substantially faster than genome alignment, without a loss in accuracy.

Results

from wand.image import Image as WImage
img = WImage(filename='../../../results/counts/total_reads_counted.pdf')
img

---------------------------------------------------------------------------
PolicyError                               Traceback (most recent call last)
/tmp/ipykernel_7623/345816063.py in <module>
      1 from wand.image import Image as WImage
----> 2 img = WImage(filename='../../../results/counts/total_reads_counted.pdf')
      3 img

~/miniconda3/lib/python3.7/site-packages/wand/image.py in __init__(self, image, blob, file, filename, pseudo, background, colorspace, depth, extract, format, height, interlace, resolution, sampling_factors, units, width)
   9324                     self.read(blob=blob)
   9325                 elif filename is not None:
-> 9326                     self.read(filename=filename)
   9327                 # clear the wand format, otherwise any subsequent call to
   9328                 # MagickGetImageBlob will silently change the image to this

~/miniconda3/lib/python3.7/site-packages/wand/image.py in read(self, file, filename, blob, background, colorspace, depth, extract, format, height, interlace, resolution, sampling_factors, units, width)
  10073             r = library.MagickReadImage(self.wand, filename)
  10074         if not r:
> 10075             self.raise_exception()
  10076             msg = ('MagickReadImage returns false, but did not raise '
  10077                    'ImageMagick  exception. This can occur when a delegate '

~/miniconda3/lib/python3.7/site-packages/wand/resource.py in raise_exception(self, stacklevel)
    223             warnings.warn(e, stacklevel=stacklevel + 1)
    224         elif isinstance(e, Exception):
--> 225             raise e
    226 
    227     def make_blob(self, format=None):

PolicyError: not authorized `../../../results/counts/total_reads_counted.pdf' @ error/constitute.c/ReadImage/412