Question: ERROR In aligmnet of RNA_seq data using STAR aligner_updated
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gravatar for akhan
11 days ago by
akhan0
United States
akhan0 wrote:

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 \
--sjdbGTFfile ./Mus_musculus.GRCm38.95.gtf --sjdbOverhang 74

#note: no problem generating the index

STAR --genomeDir ./genome --runThreadN 12 --runMode alignReads \
--readFilesIn 129X1_SvJ_FCocaine74_76_212NAC.fastq_1.gz 129X1_SvJ_FCocaine74_76_212NAC.fastq_2.gz --readFilesCommand zcat \
--genomeLoad NoSharedMemory --outFileNamePrefix ./output/star_129x1 \
--outSAMattributes All --sjdbScore 10 --outSJfilterOverhangMin 30 12 12 12



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

rna-seq alignment genome • 83 views
ADD COMMENTlink modified 11 days ago by genomax71k • written 11 days ago by akhan0

There is a thread that seems to address this problem. Use the latest stable version of STAR seems to be the solution.

If that does not work then as the error suggests you should contact Alex Dobin (author of STAR) at the email address included. Be ready to provide access to your data so he can reproduce the error.

ADD REPLYlink modified 11 days ago • written 11 days ago by genomax71k
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