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NAL-i5K / NAL_RNA_seq_annotation_pipeline

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schistocerca_compatible #58

Closed dasterix closed 1 year ago

dasterix commented 1 year ago

These changes are meant to update the pipeline to be compatible with large genomes such as those of the Schistocerca genus. Mainly this meant updating the pipeline to use .csi indeces for .bam files rather than the older .bai indeces. This allows the use of .BAM files without the size constraint of the old .bai indeces. Additionally, a small change was made to download_sra_metadata.py, avoiding an error caused by the previous query syntax which searches for a column that doesn't exist in the Schistocerca sra files.

Be sure to also update your bam_to_bigwig.py script, those changes will be pushed separately onto that repository.

dasterix commented 1 year ago

I also had to make changes to bam_to_bigwig.py. https://github.com/NAL-i5K/bam_to_bigwig/pull/3