In order to configure your analysis, make changes to config.yaml
.
SAMPLES
: A tab-separated file with the following example should be provided to specify the samples:
sample | condition | type |
---|---|---|
ETOH.R1 | EtOH | RNA |
ETOH.R2 | EtOH | RNA |
ETOH.R3 | EtOH | RNA |
DHT.R1 | DHT | RNA |
DHT.R2 | DHT | RNA |
DHT.R3 | DHT | RNA |
INPUT | DNA |
sample: Sample name
condition: Treatment condition (blank if none; blank for DNA)
type: Sample type (RNA or DNA)
UNITS
: A tab-separated file with the following example should be provided to specify the units (replicates or lanes):
sample | unit | fq1 | fq2 |
---|---|---|---|
ETOH.R1 | 1 | reads/EM_LNCaP_R1_EtOH_L1_1.fq.gz | reads/EM_LNCaP_R1_EtOH_L1_2.fq.gz |
ETOH.R2 | 1 | reads/EM_LNCaP_R2_EtOH_L1_1.fq.gz | reads/EM_LNCaP_R2_EtOH_L1_2.fq.gz |
ETOH.R3 | 1 | reads/EM_LNCaP_R3_EtOH_L1_1.fq.gz | reads/EM_LNCaP_R3_EtOH_L1_2.fq.gz |
ETOH.R3 | 2 | reads/EM_LNCaP_R3_EtOH_L2_1.fq.gz | reads/EM_LNCaP_R3_EtOH_L2_2.fq.gz |
DHT.R1 | 1 | reads/EM_LNCaP_R1_DHT_L1_1.fq.gz | reads/EM_LNCaP_R1_DHT_L1_2.fq.gz |
DHT.R2 | 1 | reads/EM_LNCaP_R2_DHT_L1_1.fq.gz | reads/EM_LNCaP_R2_DHT_L1_2.fq.gz |
DHT.R3 | 1 | reads/EM_LNCaP_R3_DHT_L1_1.fq.gz | reads/EM_LNCaP_R3_DHT_L1_2.fq.gz |
INPUT | 1 | reads/NL18_L2_1.fq.gz | reads/NL18_L2_2.fq.gz |
sample: Sample name (same as in samples.tsv)
unit: Unit no
fq1: Path to the 1st FASTQ file
fq2: Path to the 2nd FASTQ file
PRIMERS
: A tab-separated file with the following specificiations (and example row) should be provided to specify the regions of analysis:
Region name | Forward primer | Reverse primer | Chromosome | Start | End |
---|---|---|---|---|---|
overlapped_read_114 | AGCGCGGCTTAGTGA | TACCAGGAGACTATTTCCAACA | chr8 | 6456903 | 6457213 |
This file shouldn't have a header. The primers should be 5' to 3' and the positions should be BED-like (0-based).
-
REF
FA
: Path to the FASTA file of the reference genomeBWA_IDX
: Path to the BWA index files (prefix)FIXED
: Path to the FASTA file matching the wild type plasmids (or the same asFA
)
-
SEQ
UMI1_LEN
: Length of the 5' UMIUMI2_LEN
: Length of the 3' UMIEXPECTED_TLEN
: Template (insert) length of the plasmids (excluding UMIs but including primers)