CONFIG.md

Reference Flatfiles and Samples

RNA-Seq

Prepare Reference GTF/FASTA

• organism/assembly: Ensembl mus musculus release 101, mm10 (https://ftp.ensembl.org/pub/)
• ref_gtf: mus_musculus.101.mainChr.gtf
• star_index: Prepare STAR genome index as described in STAR manual

Prepare Sample FASTQ

• Copy sample FASTQ files to subfolder ./raw/

Samples: RNA-Seq 1

prefix	fastq
M2c-WT_1	Wittig_Lib_XM_M2c-WT_1_R1.fastq.gz
M2c-WT_2	Wittig_Lib_XM_M2c-WT_2_R1.fastq.gz
M2c-WT_3	Wittig_Lib_XM_M2c-WT_3_R1.fastq.gz
M2c-KO_1	Wittig_Lib_XM_M2c-KO_1_R1.fastq.gz
M2c-KO_2	Wittig_Lib_XM_M2c-KO_2_R1.fastq.gz
M2c-KO_3	Wittig_Lib_XM_M2c-KO_3_R1.fastq.gz