[IGBF-4345] m6A pipeline one more time! - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
2
Epic Link:
Support NSF pollen grant
Sprint:
Fall 6, Fall 7

Description

GOAL: To run the m6a PIpeline again with the hope of finding sites in the 3' UTR region.

Kausik had his grad student produce more DART seq data.

https://drive.google.com/drive/folders/1Q_RjN1kX5jXxfNbKzPs9ErIMsE5aSf3M?usp=sharing

Data going onto the cluster location =
/projects/chakrabartilab/fnb0/plasmodium/dart2

The end desire of finding m6a sites in those 3'UTR regions.....

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Robert Reid created issue - 28/Oct/25 11:12 AM

Robert Reid made changes - 28/Oct/25 11:12 AM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

Robert Reid made changes - 03/Nov/25 10:01 AM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Brandon Bendickson added a comment - 05/Nov/25 10:43 AM - edited

Wait for Dr. Reid's Bullseye run before proceeding.

Pipeline steps:
1. Align new sequences with BWA-Mem: Done
2. Convert new Bams to Beds: Done
3. Write script that does the following:

Read in Pfalciparum fasta (forward/reverse)
Read in new bed file into a list of lists [(chromosome, align start, align end, strand), ...]
read and parse 3' Pfalciparum gff file and store Chromsome, UTR start, UTR end, GeneID, and strand
Using 3' UTR coords, pull the sequenced of those portions from fasta
If the alignment start falls into the UTR range, save all associated data/sequences
Manually search matched 3' region sequences for m6A RAC motif and record coords.
4. Iterate for all beds
5. Share results

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Brandon Bendickson added a comment - 05/Nov/25 10:43 AM - edited Wait for Dr. Reid's Bullseye run before proceeding. Pipeline steps: 1. Align new sequences with BWA-Mem: Done 2. Convert new Bams to Beds: Done 3. Write script that does the following: Read in Pfalciparum fasta (forward/reverse) Read in new bed file into a list of lists [(chromosome, align start, align end, strand), ...] read and parse 3' Pfalciparum gff file and store Chromsome, UTR start, UTR end, GeneID, and strand Using 3' UTR coords, pull the sequenced of those portions from fasta If the alignment start falls into the UTR range, save all associated data/sequences Manually search matched 3' region sequences for m6A RAC motif and record coords. 4. Iterate for all beds 5. Share results

Ann Loraine made changes - 09/Nov/25 3:03 PM

Sprint

Fall 6 [ 229 ]

Fall 6, Fall 7 [ 229, 230 ]

Ann Loraine made changes - 09/Nov/25 3:03 PM

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