Run¶
TIDAL1.2 can be run from both sra and fastq format, when library name and length is provided.
TIDAL from SRA¶
To run TIDAL on sra file, there are two you have to do two things:
Prepare a run file
Format of run file (tab delimited)
Library_ID SRR_Accession Min_Library_Length
S2R+ SRR497719 100
OSS_C SRR1185816 150
The first column header should be Library_ID, this used to skip the header line. The Library ID is used to name output files. The SRR Accession is used to download the file.
2. Run TIDAL_from_sra.sh
nohup /location_from_root/TIDAL/CODE/TIDAL_from_sra.sh run_file.txt &
TIDAL from fastq¶
To run TIDAL on fastq file, we need the library in fastq format and read length.
nohup /location_from_root/TIDAL/CODE/TIDAL_from_fastq.sh libname.fastq min_len &
# libname.fastq : DNA seq library
# min_len : read length
WARNING: the library filename should have *.fastq suffix. The code will not work with *.fq suffix.
Congratulations!!! You have managed to run TIDAL, hope you get exciting results!