README.md

TET2 manuscript code

QC and adapter/quality trimming

1. Fastqc - script like qc.sh but for untrimmed files
2. Use fastp.sh to remove adapters and filter based on quality
3. qc.sh - check quality, if adapters were removed

Mapping

4. star_index.sh - create an index file for star
5. map_array.sh - map reads to reference
6. samtools stats qc of bam files to check the quality of mapping

Retriving counts

7. featureCounts_all.sh - get counts of reads mapped to reference genes

Differential analysis

8. analysis/differential_expression.R - script for differential analysis using DEseq2 with firther pathways analysis.

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Variables that need to be exported befor running the code:

export curdir=/path/to/this/repo export raw=$curdir/raw

Notes

• Downstream bcr analysis is saved in https://github.com/mariamurach/bcr_R and uses output files from bcr_analysis.R

• Paths in the code files were anonymized and might require editing to fit users file stracture

• This pipeline uses code https://github.com/liulab-dfci/RIMA_pipeline to retrive CDR3 information and to concatenate bcr files from TRUST4 output.