Tag: genomeGenerate

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 \…

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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,…

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Indexing the reference genome

Indexing the reference genome 0 nohup STAR –runMode genomeGenerate \ –genomeDir /Users/yasi/mockexp/genome/genome_index/ \ –genomeFastaFiles /Users/yasi/mockexp/genome/GCF_000001405.39_GRCh38.p13_genomic.fna\ –sjdbGTFfile /Users/yasi/mockexp/genome/genomic.gtf –sjdbOverhang 80 > star_genome_generate.log 2>&1 What I am missing or doing wrong while trying to index the reference genome with STAR? STAR indexing genome • 47 views Read more here: Source link

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AWS STAR Genome Index Error

AWS STAR Genome Index Error 0 Hello, I have been trying to run this line of code for the longest time: STAR –runThreadN 20 –runMode genomeGenerate –genomeDir genomeDir/ –genomeFastaFiles Homo_sapiens.GRCh38.dna.toplevel.fa –sjdbGTFfile Homo_sapiens.GRCh38.110.chr.gtf I first tried running it on my home terminal but then realized that that it would take several…

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Converting from BED to SAF/GFF

I believe that SAF format use 1-based coordinates that are closed on both ends. Here is how I got this conclusion. First make some toy data. $ cat genome.fa >chr1 AATTCCGGAAAATTTTCCCCGGGGAAAAAAAAAAAAAAAAAACCCCCCCCCCCCCCCCCCCCCCCCCCCC $ cat reads.fa >q1 AAAATTTTCCCCGGGGAAAAAAAAAAAAAAAAAACC Map reads to the genome: $ STAR –runMode genomeGenerate –genomeDir test_star –genomeFastaFiles genome.fa –genomeSAindexNbases…

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STAR Genome index Error

STAR Genome index Error 0 I tried to run STAR command for RNAseq but I got the following error. /home/pshekar/RNAseq/STAR-2.7.11a/source/STAR –runMode genomeGenerate \ –genomeDir GRCh38.79.chrom1 \ –genomeFastaFiles genome/Homo_sapiens.GRCh38.dna.chromosome.1.fa \ –sjdbGTFfile gtf/Homo_sapiens.GRCh38.79.chrom1.gtf \ /home/pshekar/RNAseq/STAR-2.7.11a/source/STAR –runMode genomeGenerate –genomeDir GRCh38.79.chrom1 –genomeFastaFiles genome/Homo_sapiens.GRCh38.dna.chromosome.1.fa –sjdbGTFfile gtf/Homo_sapiens.GRCh38.79.chrom1.gtf –sjdbOverhang 62 –sjdbOverhang 62 *!!!!! WARNING: –genomeSAindexNbases 14 is…

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Ubuntu exits (Cellranger mkref, custom reference)

Hello, I am trying to generate a custom mouse reference genome that includes 3 transgenes (eGFP, tdTomato, and Cre), I have added these to the reference genome and the gtf as well as filtered the gtf with no issues. When I run mkref (usung Ubuntu within windows, version 2204.2.33.0), it…

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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…

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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…

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CellRanger problem

Hey, what’s up? I’m using the CellRanger for scRNA and this problem appears: Generating STAR genome index (may take over 8 core hours for a 3Gb genome)… Jun 07 19:02:11 ….. started STAR run Jun 07 19:02:11 … starting to generate Genome files Jun 07 19:02:11 … starting to sort…

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Query in indexing human genome

Hello , I have to do RNAseq analysis of human cancer cell lines , for that I need to index human genome , as a refrence genome. I index the human genome gff file from thr NCBI.. during some lecture I have heard that ncbi human genome file has some…

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Some questions about gencode.v43.transcripts.fa and pacbio data

Hi Alexander, I want to map gencode.v43.transcripts.fa to GRCh38.primary_assembly.genome.fa, but I failed with STAR and STARlong, and the generated Aligned.out.bam is particularly small, I don’t understand why this happens I don’t understand why there is such a problem, so I’m here to ask you for advice. Thank you very much…

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Using STAR for RNA seq-alignment.

Using STAR for RNA seq-alignment. 1 Hello All! I am trying to map the RNA seq data with the reference genome using STAR aligner tool in cluster. I used the reference fasta file and gtf file to create the genomeDirectory that has the genome index. Now, I want to map…

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STAR –runMode error

STAR –runMode error 0 I have the most up to date STAR installed (not star) with the correct genome and gtf file yet it is saying runMode doesn’t exist. Any help is appreciated CODE: $ STAR –runMode genomeGenerate –genomeDir index –genomeFastaFiles Sus_scrofa.Sscrofa11.1.dna_sm.primary_assembly.1.fa –sjdbGTFfile Sus_scrofa.Sscrofa11.1.108.gtf RNAseq STAR • 57 views •…

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STAR is running but .sam file size does not increase after hours mapping

STAR is running but .sam file size does not increase after hours mapping 0 Hi there, I’m using STAR with a small genome. My samples are paired. The commands are: For genome indexes STAR –runThreadN 20 –runMode genomeGenerate –genomeDir /path/to/folder/Analyses/STAR/ –genomeFastaFiles /path/to/genome_reference/genome.fna –readFilesCommand zcat path/to/folder/with/giz_samples/R1.fq.gz R2.fq.gz –sjdbGTFfile path/to/genome_reference/genome.gff –genomeSAindexNbases 11…

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ouput files after GenomeGenerate

Dear Dr Dobin, I’m a biologist learning how to do Bio-informatics. GCF_000001405.40_GRCh38.p14_genomic.fna genomic.gff I used 2 different machines to do it, my home computer (8 cores, 16G RAM w/ Linux) and a server from my lab.  Using the server, I used the default parameters with GenomeGenerate, whereas on my computer…

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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…

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MARS seq alingment

MARS seq alingment 0 Hello everyone, new here and also new to the field. was asked to create a pipeline for RNA seq and after two months of self learning of how to interact with each code im stuck with the program STAR. what im trying to do for now…

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Indexing with STAR

Indexing with STAR 0 Hello, I am working with RNA seq data and creating an index of reference genome Gossypium hirsutum by using STAR. STAR asks GTF annotation format while my file is GFF3. According to literature, in order to run GFF file I need to remove –sjdbOverhang 50 and…

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How to download the Homo_sapiens.GRCh38.100.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa files for my analysis?

How to download the Homo_sapiens.GRCh38.100.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa files for my analysis? 0 I am trying to perform STAR alignment and I need the reference files for indexing. I would like to know how to download the Homo_sapiens.GRCh38.100.gtf and Homo_sapiens.GRCh38.dna.primary_assembly.fa files so that I can use my following code for indexing…

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STAR Genome Indexing

STAR Genome Indexing 0 One of the arguments that STAR –genomeGenerate takes in is sjdbOverhang which the manual says “specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database” and that it should be equal to read length – 1….

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STAR rna-seq for bacterial genomes

Hi, I’m willing to use STAR for bacterial genomes. I wanted to ask if this is strongly unadvised or if there is a way to manage the main challenges of mapping reads to prokaryotes. (I know there are specific tools for this purpose, i.e. EdgePro, but I’m a beginner in…

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