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NAL-i5K / NAL_RNA_seq_annotation_pipeline

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Add bam to cram conversion #50

Open mpoelchau opened 3 years ago

mpoelchau commented 3 years ago

We are exploring moving to cram format from bam to save space. @debbiedai can you create a new branch that does the following:

  1. add samtools view input.bam -o <output.cram> -C -T <genome.fasta> --level=9 to RNAseq_annotate.py. The input bam file would be from here: https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/blob/master/rnannot/RNAseq_annotate.py#L518

  2. Rename the cram output file in the same style as https://github.com/NAL-i5K/NAL_RNA_seq_annotation_pipeline/blob/master/rnannot/RNAseq_annotate.py#L532

  3. Add the cram file to add_trackList.py (I need to provide more information on how to add to the trackList.json file)

  4. Remove the bam file and bam.bai file information from add_trackList.py