LongReads: Implement methylation

imgag / megSAP

a Medical Genetics Sequence Analysis Pipeline

GNU General Public License v3.0

67 stars 18 forks source link

Open leonschuetz opened 1 year ago

leonschuetz commented 1 year ago

leonschuetz commented 12 months ago

leonschuetz commented 11 months ago

Tool for annotation: ZipperBams

steps new analysis:

unaligned BAM --> FastQ --> minimap --> ZipperBams --> sort (-->del unaligned BAM + Fastq)
steps reanalysis:

BAM --> FastQ --> minimap --> ZipperBams --> sort (-->del BAM + Fastq)

leonschuetz commented 11 months ago

On hold till Nvidia-Benchmark

leonschuetz commented 9 months ago

new Dorado version creates mapped BAM with methylation

leonschuetz commented 9 months ago

come up with a solution to display methylation:

ubuntolog commented 9 months ago

remapping with dorado

leonschuetz commented 7 months ago

Did anybody tested this? Seems to solve the (re-)mapping issues with methylation.

@jakobmatthes @caspargross

leonschuetz commented 7 months ago

First tests seem to work

leonschuetz commented 5 months ago

implemented in Branch lr_methylation

caspargross commented 5 months ago

Started test in /mnt/storage1/projects/research/23064_1267_MSS_ONT

caspargross commented 5 months ago

Everything works! Phasing of known imprinted gene (SNRPN) is correct. From my side you can close and merge the issue.

jakobmatthes commented 5 months ago

[x] implement modkit for postprocessing BAM with methylation
[ ] add QC parameters
- [ ] average methylation percentage
- [ ] quality (Q score) for modified bases calls

leonschuetz commented 5 months ago

jakobmatthes commented 5 months ago

[x] check if merge_samples supports multilpe mod.unmapped.bam files, multiple mapped BAM files (correct BAM to "FASTQ" conversion/BAM to BAM conversion), see sample 21073LRa266

leonschuetz commented 4 months ago

leonschuetz commented 2 months ago

leonschuetz commented 1 week ago

[x] Add tool to extract methylation from modkit calls -> ExtractMethylationData