rna-star

Hello all, I am putting together a workflow using the STAR aligner. I'm wondering if there are

Hi Ellen, yes, all parameters should appear in the Log.out file. It's always a good idea to check

Hi, I would recommend using the default value (100). This parameter has typically only very marginal

Hi Yixuan, you would need to figure out which reads cross this junction, and then look at their

Hi Vitor, we have a paper describing this approach and its advantages here: https://genome.cshlp.org/

Great, thanks for the confirmation! On Thursday, May 4, 2023 at 2:26:27 PM UTC-6 Alexander Dobin

Try to reduce the number of threads, let's say 16 or something. STAR throws errors with higher

Hi, Alex I did change the annotation string as in attached file and it worked for Gencode annotation.

Hi Alex, Thanks for the clarification! Can you please suggest additional flags or parameters that we

Hi @nalghamd88 please use the latest version of STAR, older versions do not support this option. On

Please post FusionInspector questions on the GitHub: https://github.com/FusionInspector/

Hi Niharika, I'm sorry to bother you. my name is Qiqi Guo and I'm a postdoctoral researcher

Hi Alexander, I want to map gencode.v43.transcripts.fa to GRCh38.primary_assembly.genome.fa, but I

Hi Larraitz, please specify full path to STAR executable. On Thursday, March 16, 2023 at 2:34:35 PM

That's amazing, thanks for this information. On Wednesday, February 22, 2023 at 11:39:56 AM UTC-5

Hi Assa, --soloType SmartSeq requires specifying cell IDs. It's easiest to do it in the --

Hi, I get a Segmentation fault (core dumped) during mapping with starsolo, using star 2.7.10b. Any

Hi Ryan, Which parameters did you map this sample with when it was successful? I would recommend

Hi Ryan, For unknown strand, you can use . (dot) symbol. Cheers Alex On Saturday, February 11, 2023

Hi, For the human genome, I recommend using the FASTA and GTF from Gencode or Ensembl. They have

Hi Paul, please switch to the latest version of STAR: https://github.com/alexdobin/STAR/releases/tag/

Hi Matteo, I think the no-mismatch requirement is not needed - STAR chooses the best-scoring

Hi Matteo, You are correct: GeneCounts output always counts only unique mappers - it does not depend

Hi Assa, the reads are short to begin with, and the mapped portion of the reads that could map is

HI, I've been trying yo run STARSolo, matching Cell Rager 7.0.x results as follows; #!/bin/bash

Hi Ryan, that's correct; the novel junctions from the 1st pass inserted in the genome for the 2nd

Thank you. I've tried a number of variations of these but have not had any success. I will have

Hi Z, it seems it could not allocate ~30GB. Please try to increase it (before STAR run) with ulimit -

Hi, I am running STARsolo enabling the counting of multi--gene UMI (--soloMultiMappers EM). I was

Never mind, I solved the problem. Another issue happens, the mapping speed is too slow. Is there any