Pipeline

1. Fastqc to see the quality of raw fastqc reads

2. Trimmomatic to trim the adapters

3. python /home/xzhen/pipelines/slamseq/submit_slamdunk.py --in-dir pytest --reference GRCm38.p6.genome.fa --bed UTR/3pUTR.bed --out-dir pytest

4. cp out_dir//count/.tsv /output

5. prepare a list of sample names

6. Rscript prepare_for_netbid2.R

7. Further NetBID analysis

Alleyoop and NetBID