Hi,

I am new to a lot of the bioinformatic tools that are available to do the alignment of RNA-seq data. Currently, I am using STAR aligner to do some alignment on my data. I have successfully created a genome index and aligned my data using the following commands

STAR --runMode --runThreadN 30 genomeGenerate --genomeDir ./mouse_genome_test/SJ_index --genomeFastaFiles ./mouse_genome_test/Mus_musculus.GRCm38.dna.primary_assembly.fa \ --sjdbGTFfile ./mouse_genome_test/Mus_musculus.GRCm38.95.gtf --sjdbOverhang 74

STAR --genomeDir ./ --runThreadN 12 --runMode alignReads --outSAMtype BAM SortedByCoordinate Unsorted \ --outFilterMultimapNmax 1 --quantMode GeneCounts --twopassMode Basic \ --outFileNamePrefix ./star_129X1PFC \ --readFilesIn 129X1_SvJ_FCocaine74_76_212NAC.fastq_1.gz 129X1_SvJ_FCocaine74_76_212NAC.fastq_2.gz \ --readFilesCommand zcat --sjdbGTFfile ./Mus_musculus.GRCm38.95.gtf --sjdbOverhang 74

However, I am trying to use a pipeline that was in the paper (https://www.biorxiv.org/content/biorxiv/early/2014/09/04/008763.full.pdf) follows and I get an error which shown below the commands. I am not quite sure what is the error. To me, it should not generate any error. Anyone help with this issue would be greatly appreciated

STAR --runMode genomeGenerate --genomeDir ./genome --genomeFastaFiles ./Mus_musculus.GRCm38.dna.primary_assembly.fa \ et--sjdbGTFfile ./Mus_musculus.GRCm38.95.gtf --sjdbOverhang 74

EXITING because of FATAL BUG: unknown/unimplemented SAM attribute (tag): 16 SOLUTION: contact Alex Dobin at dobin@cshl.edu

Sep 10 14:18:05 ...... FATAL ERROR, exiting

Arshad