Questions tagged [star]

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2answers
47 views

Importance of Proper Pairs vs Aligned Reads for RNASeq data

I have stranded, paired end RNASeq reads that I have aligned using STAR. I plan do conduct a differential expression analysis with DESeq2. After running quality control checks, a good portion of my ...
1
vote
1answer
20 views

Why I am getting different gene lengths for the same genes in different samples with rsem-calculate-expression?

I am running the STAR-RSEM pipeline, I have a simple shell script(*), which I use to loop over fasta files corresponding to different samples. From the output, I am ...
1
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2answers
38 views

Extract mapping coverage from GTF files

I am doing paired end RNA-seq analysis. I used STAR mapper and then StringTie for getting quantification of my data. After successfully running StringTie, I got .gtf...
2
votes
0answers
142 views

What could cause differing counts of R1 and R2 in Paired End Sequencing (RNASEQ)

I recently finished mapping an RNAseq run using STAR2.3.0 and noticed the read1 and read2 counts are different, according to samtools flagstat. The map% is ~80% but the R1 R2 counts are: R1=...
0
votes
1answer
356 views

STAR Indexing Diference for Small and Large Genome File Output

I have a quick doubt on the output of the Genome Indexing, I have used the STAR program along with genome .fasta file and GFF file. Genome size is 3GB, here is the file output ...
2
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1answer
785 views

Disk space error while aligning reads using STAR

Hi am trying to align RNA-seq reads using STAR through following commands, ...
3
votes
2answers
738 views

Error creating indices using STAR

I am trying to index wheat genome using STAR through following command ...
2
votes
1answer
451 views

What process and input data is required for a cellranger reference transcriptome?

I'm analysing single-cell RNA-Seq data using the 10X Genomics cellranger platform. While they provide reference data for Mouse and Humans, other species require a ...
0
votes
1answer
172 views

Why is my STAR reference genome indexing aborting on my GNU/Linux server but not on my Mac OS X laptop?

I am running the following command to index my genome: ...
2
votes
1answer
1k views

Can I index a compressed FASTA file using STAR?

I am using STAR to align RNA-seq reads to a reference genome. Before the alignment, I need to generate an index of the reference genome. I use the following code to generate the index successfully: <...
6
votes
1answer
600 views

STAR-long parameters for aligning RNA ONT reads to genome

Are there any suggested parameters to align ONT reads to the reference genome using STAR-long? For now, I used the parameters suggested here, but I noticed a weird behaviour. I have RNA reads (D. ...
8
votes
2answers
396 views

Building STAR Genome Index for nanopore RNA sequencing

I am aligning a dataset of 1,000,000 reads oh human mRNA sequenced on Oxford Nanopore Technologies' MinION, and would like to use the STAR aligner, using the parameters recommended by Pacific ...
10
votes
1answer
524 views

Quantifying reads mapping to multiple loci

I have been using STAR for our RNA-Seq samples. The final.out log file reports percentage of uniquely mapped reads along with percentage of reads that map to ...