I'm trying to align reads from a study but they have aligned it to hg18. I managed to get the hg18.fa file in and want to align the samples to it. The code I am using is:
for i in *.fq.gz; do STAR --./hg18.fa --runMode alignReads --readFilesIn $i --readFilesCommand zcat --outSAMtype BAM SortedByCoordinate --chimSegmentMin 20 --quantMode GeneCounts --outReadsUnmapped Fastx --outFileNamePrefix ./read_out2/$i; done
However, this is failing as error messages are occuring such as
EXITING: FATAL INPUT ERROR: empty value for parameter "./hg18.fa" in input "Command-Line-Initial" SOLUTION: use non-empty value for this parameter
I assume this is because it is not annotated and indexed. When looking online I am trying to find annotations but cannot find it clearly.