Tag: genomeLoad

Bam files generated with STAR cause a segmentation fault core dump error when used with another tool

I am mapping RNA-Seq data using STAR, using multi-sample two-pass mapping. I first mapped all samples with one-pass then concatenated their SJOut files and filtered junctions. I launched the second mapping by using this SJOut file. I used this command to generate genome : ` /home/STAR-2.7.10b/bin/Linux_x86_64/STAR \ –runThreadN 10 \…

Continue Reading Bam files generated with STAR cause a segmentation fault core dump error when used with another tool

RNA star taking more than 24h to complete 2nd pass

RNA star taking more than 24h to complete 2nd pass 0 Hello all, I am very new to star alignment and rna seq in general. I have 20 mouse rna bulk samples which I am trying to align to a reference genome, after performing QC filtering and trimming. To align,…

Continue Reading RNA star taking more than 24h to complete 2nd pass

STAR Intron Motif Script Gives Segmentation fault Error

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…

Continue Reading STAR Intron Motif Script Gives Segmentation fault Error

STAR Script Add a `//` Error

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”…

Continue Reading STAR Script Add a `//` Error

Utilization of STAR Output for RNA-seq Analysis

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…

Continue Reading Utilization of STAR Output for RNA-seq Analysis

A question about the raw RNA-seq processing workflow

“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…

Continue Reading A question about the raw RNA-seq processing workflow

How to create Dockerfile without copying large data input and Build image such that snakemake wokflow run as Entrypoint

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…

Continue Reading How to create Dockerfile without copying large data input and Build image such that snakemake wokflow run as Entrypoint

mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

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…

Continue Reading mapping – STAR error in snakemake pipeline: “EXITING because of FATAL ERROR: could not open genome file”

[STAR] How to clear memory after lost –genomeLoad

[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…

Continue Reading [STAR] How to clear memory after lost –genomeLoad