isomiR annotations wrong
The coordinates of the isomiR annotations prepared in the PREPARE workflow are (almost?) all wrong.
Example from the first six entries from file isomirs_annotation.bed
generated by a test/test_workflow_slurm.sh
run:
1 -2 -1 MIMAT0027619 . - . miRNA . ID=MIMAT0027619;Alias=MIMAT0027619;Name=hsa-miR-6859-3p_5p-1_3p-1;Derives_from=MI0022705
1 -2 -1 MIMAT0027618 . - . miRNA . ID=MIMAT0027618;Alias=MIMAT0027618;Name=hsa-miR-6859-5p_5p-1_3p-1;Derives_from=MI0022705
1 -2 -1 MIMAT0005890 . + . miRNA . ID=MIMAT0005890;Alias=MIMAT0005890;Name=hsa-miR-1302_5p-1_3p-1;Derives_from=MI0006363
1 -2 -1 MIMAT0049032 . - . miRNA . ID=MIMAT0049032;Alias=MIMAT0049032;Name=hsa-miR-12136_5p-1_3p-1;Derives_from=MI0039740
1 -2 -1 MIMAT0004571 . + . miRNA . ID=MIMAT0004571;Alias=MIMAT0004571;Name=hsa-miR-200b-5p_5p-1_3p-1;Derives_from=MI0000342
1 -2 -1 MIMAT0000318 . + . miRNA . ID=MIMAT0000318;Alias=MIMAT0000318;Name=hsa-miR-200b-3p_5p-1_3p-1;Derives_from=MI0000342
As a consequence, the isomiR quantification in the QUANTIFY workflow test fails. It was therefore disabled until this issue is resolved.
To do:
-
Fix the preparation of isomiR annotations (correct coordinates) -
Reenable isomiR quantification in the tests.
Edited by Alex Kanitz