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MAF.zip 2026-07-08 93.3 kB
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Version history


---
version : 2026-07-08

major

further developed microRNA and mRNA scripts
 33_se_mir_algo_comparison.sh
 33_se_mrna_algo_comparison.sh

in R_import_scripts
 improved scripts:
 main_v2.R
 quant.import_v2.R
 and an additional mapping table for the new examples above
 mapTable2.mir.trna.tsv
 (do not mixup with the existing one: mapTable.mir.trna.tsv
  which is still valid)

minor

adjusted
 30_top_wrap.sh


---
version : 2026-03-09
 R_import_scripts - corrected
 main.R
 quant.import.R
 

---
version : 2026-03-04
 path problem in bash script 31_se_mir.sh solved
 added one new bash script 32_se_mir.sh
  using UMICollapse instaed of umi_tools
 

---
version : 2025-07-15
 dependency bugs in R import scripts solved
 added two missing R scripts
 

---
version : 2025-07-09

a new bash script based on 31_se_mir.sh from Karthik Nair
 optimized for large number of samples
 and condensed to a core workflow
 in MAF/bin/mir_optimized/31_mirna_core_optimized.sh


---
version : 2025-07-02

bash scripts adjusted, bugs removed
 bash script version changed from 30 to 31 in some cases
R script : qname_srv.uni.R : bug removed
samtools markdup : removed from the options as it assumes the postion #8 of a colon separated qname string
 it needs more efforts to be re-integrated again
bbmap alignment call adjusted
 to not generate an extended and therefore for the workflow wrong  qname


---
version : 2025-06-17

Publication

Zhao X, Korsching E. Evaluating the Effectiveness of Various Small RNA Alignment Techniques
in Transcriptomic Analysis by Examining Different Sources of Variability
Through a Multi-Alignment Approach. Methods and Protocols. 2025; 8(3):65.
https://doi.org/10.3390/mps8030065
Source: 0_readme_version_history.txt, updated 2026-07-08