Tag: genomeLoad

STAR Intron Motif Script Gives Segmentation fault Error 0 I have the following inputs: # Define input directory containing FASTQ files Input_directory=”/path/to/fastq/folder” # Define output directory for STAR output files Output_directory=”/path/to/output/directory” # Define paths to reference files Annotation_GTF=”/path/to/Zebra/fish/GRCz11.110.chr.gtf” Genome_FASTA=”/path/to/soft/masked/Zebra/fish/primary_assembly.fa” Reference=”/path/to/soft/masked/STAR/created/reference/only/for/use/with/STAR” # Define the number of threads to use num_threads=4 To…

STAR Script Add a `//` Error 1 My script has a couple of variables pre-defined: # Path to the genome FASTA file from Illumina iGenomes For Danio rerio (in this case): Genome_FASTA=”path/to/genome.fa” # Path to the annotation GTF file: Annotation_GTF=”path/to/Danio_rerio.GRCz11.110.chr.gtf” # Path to the input directory containing FASTQ files: Input_Directory=”/path/to/FQ_Folder”…

Utilization of STAR Output for RNA-seq Analysis 0 Hello, I am a novice graduate student conducting RNA-seq analysis. The following are the results obtained using the STAR code. # STAR STAR \ –readFilesIn run_clean_1.fastq.gz run_clean_2.fastq.gz \ –genomeDir STAR_genomeGenerate \ –readFilesCommand zcat \ –runThreadN 10 \ –twopassMode Basic \ –outFilterMultimapNmax 20…

“Hello, I am a student who recently started studying bioinformatics. Since my understanding is still limited, I would appreciate it if you could explain even if the difficulty of the question is low. I am currently working with RNA-seq data and I am facing batch effects that are not reduced…

How to create Dockerfile without copying large data input and Build image such that snakemake wokflow run as Entrypoint 1 I have project folder structure like Below : which has size of more than 50 GB . When i am creating Dockerfile such that Snakefile workflow which utilizes data from…

I’m trying to use a 2 pass STAR mapping strategy (also explained here informatics.fas.harvard.edu/rsem-example-on-odyssey.html), but I’m getting an error. I’ve read through this page [https://github.com/alexdobin/STAR/issues/181] and I have a similar issue, but the discussed solutions don’t seem to help. Perhaps this is more a snakemake issue rather than a STAR…

[STAR] How to clear memory after lost –genomeLoad 1 Hi all, I’m regularly using STAR and happen to play with the argument –genomeLoad. My problem is that I think a genome index is still loaded in memory but I can’t find it (I tried to –genomeLoad Remove all the indexes…