Tag: sjdbOverhang

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,…

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

Indexing human chromosome assembly of GRCh38.p14 using STAR 1 I want to index the genome assembly “GRCh38.p14” before aligning to my reads. however one parameter that STAR needs is the overhang length –sjdbOverhang ReadLength-1I only have the chromosome assembly and the gtf file, how should I find out what is…

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…

Mapping RNA-Seq reads onto viral genome 0 Hi everyone, I have 6 files of paired-end 75 nt RNA-Seq reads from HEK293 I want to map onto the AAV genome. I got the reference genome as a fasta file and the annotation file as gff3/gtf from NCBI. For mapping onto the…

Sjdboverhang Option In Star 2 I have some difficulties in understanding the option sjdbOverhang in STAR. This option is set when making use of a splice junctions database. The manual defines it to be: “the length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length –…

“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…

Alignment of case vs. control from different origin 0 Hi Biostars! I am coming to you with a relatively simple question, but one that i have surprisingly not found and answer to. I am working with a case-cohort of samples that were prepared for RNA-seq as paired reads with a…

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…

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….

scRNAseq STAR create index how to set –sjdbOverhang 0 hello everyone, I want to create index before align read using STAR, the sjdbOverhang is described as ReadLength-1, so does it mean I should set 149 if the data is from Illumina 2×150bp？ thanks scRNAseq STAR sjdbOverhang • 12 views Source…

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…