Tag: genomeGenerate

“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…

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…

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…

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…

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…

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 •…

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…

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…

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…

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…

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…

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…

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….

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…