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Minor improvements #5

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byee4 opened this issue Jan 19, 2023 · 0 comments

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byee4 commented Jan 19, 2023 •

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Capitalize 'Snakefile' as this is the default file that Snakemake looks for
Add 'xmltodict' package (see ModuleNotFoundError in piechart.py environment #4)
Remove hardcoded "/oasis/tscc/scratch/eczhang/larp6/larp6_GRCh38/results/" from Snakefile and add to config.yaml
In config.yaml, let's actually use the bam file instead as inputs, and modify Snakefile accordingly (eg.

SAMPLES:
  - /oasis/tscc/scratch/eczhang/larp6/larp6_GRCh38/results/LARP6.CTRL_IN1.umi.r1.fq.genome-mapped.bam
  - /oasis/tscc/scratch/eczhang/larp6/larp6_GRCh38/results/LARP6.CTRL_IN2.umi.r1.fq.genome-mapped.bam
  - ...

If we can, let's add another step: try using this database (this is the 'protein' version of the nonredundant database): /projects/ps-yeolab3/bay001/annotations/nr/nr. The idea is that instead of telling us just which species has the best alignment, perhaps we can tell which protein our reads are aligning to. The command and environment will be similar, except instead of "blastn" we will want to use "blastx" along with this new database.

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