REDItoolBlatCorrection.py requires gfServer and gfClient programs from Blat package . Reference fasta file can be converted in .2bit format using the utility faToTwoBit.
REDItoolBlatCorrection.py -i rnaseq.bam -f reference.fa -F reference.2bit -o BlatCorrection -V -T
Options:
-i BAM file
-I Sort input BAM file
-f Genomic fasta file
-F Genomic fasta file in 2bit format for gfServer
-t Num. of working threads [1]
-o Output Folder [BlatCorrection_XXXX]
-k List of chromosomes to skip separated by comma or file
-r Regions in GFF in which Blat will be launched
-s Sort GFF (if unsorted). It requires grep and sort unix executables.
-q Minimum quality score [25]
-Q Fastq offset value [33]
-V Verify if gfServer is alive
-T Stop gfServer at script end
-h Print the help