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Welcome to the general user group for STAR, RNA-seq aligner.
Please be patient when submitting your
first post
- I have to moderate them to avoid junk mail.
Please check
https://github.com/alexd
obin/STAR
for details.
Most stable release:
https://github
.com/alexdobin/STAR/releases/t
ag/2.7.6a
Most recent release:
https://github.com/al
exdobin/STAR/releases/tag/2.7.
8a
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Joshua Mincer
May 22
STAR --runThreadN benefit plateau?
Hello all, I am putting together a workflow using the STAR aligner. I'm wondering if there are
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STAR --runThreadN benefit plateau?
Hello all, I am putting together a workflow using the STAR aligner. I'm wondering if there are
May 22
Ellen NM
,
Alexander Dobin
2
May 22
STAR reading command options --winAnchorMultimapNmax --outFilterMultimapNmax
Hi Ellen, yes, all parameters should appear in the Log.out file. It's always a good idea to check
unread,
STAR reading command options --winAnchorMultimapNmax --outFilterMultimapNmax
Hi Ellen, yes, all parameters should appear in the Log.out file. It's always a good idea to check
May 22
Joshua Mincer
,
Alexander Dobin
3
May 19
Samples with variable read lengths and genome index.
Hi, I would recommend using the default value (100). This parameter has typically only very marginal
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Samples with variable read lengths and genome index.
Hi, I would recommend using the default value (100). This parameter has typically only very marginal
May 19
Yixuan Wan
,
Alexander Dobin
2
May 16
No counts from SJ.out.tab
Hi Yixuan, you would need to figure out which reads cross this junction, and then look at their
unread,
No counts from SJ.out.tab
Hi Yixuan, you would need to figure out which reads cross this junction, and then look at their
May 16
Vitor Rezende da Costa Aguiar
,
Alexander Dobin
2
May 4
STARconsensus
Hi Vitor, we have a paper describing this approach and its advantages here: https://genome.cshlp.org/
unread,
STARconsensus
Hi Vitor, we have a paper describing this approach and its advantages here: https://genome.cshlp.org/
May 4
Joshua Mincer
,
Alexander Dobin
3
May 4
Mycoplasma contamination and genome generation
Great, thanks for the confirmation! On Thursday, May 4, 2023 at 2:26:27 PM UTC-6 Alexander Dobin
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Mycoplasma contamination and genome generation
Great, thanks for the confirmation! On Thursday, May 4, 2023 at 2:26:27 PM UTC-6 Alexander Dobin
May 4
Deepa Ramasamy
, …
Manjunatha B K
3
May 3
ERROR in RNA STAR
Try to reduce the number of threads, let's say 16 or something. STAR throws errors with higher
unread,
ERROR in RNA STAR
Try to reduce the number of threads, let's say 16 or something. STAR throws errors with higher
May 3
Yu Chen
, …
Алима Галиева
13
May 3
Adding custom genes
Hi, Alex I did change the annotation string as in attached file and it worked for Gencode annotation.
unread,
Adding custom genes
Hi, Alex I did change the annotation string as in attached file and it worked for Gencode annotation.
May 3
Molly H
,
Alexander Dobin
3
May 2
Trouble Matching STARSolo to CellRanger with 10X Multiome v1
Hi Alex, Thanks for the clarification! Can you please suggest additional flags or parameters that we
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Trouble Matching STARSolo to CellRanger with 10X Multiome v1
Hi Alex, Thanks for the clarification! Can you please suggest additional flags or parameters that we
May 2
Norah Alghamdi
,
Alexander Dobin
2
May 2
unrecognized parameter
Hi @nalghamd88 please use the latest version of STAR, older versions do not support this option. On
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unrecognized parameter
Hi @nalghamd88 please use the latest version of STAR, older versions do not support this option. On
May 2
Jomar S
,
Alexander Dobin
2
May 2
Error in chr discrepancy when running FusionInspector
Please post FusionInspector questions on the GitHub: https://github.com/FusionInspector/
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Error in chr discrepancy when running FusionInspector
Please post FusionInspector questions on the GitHub: https://github.com/FusionInspector/
May 2
Niharika Singh
, …
QIQI GUO
3
Apr 17
could not open file pGe.sjdbGTFfile
Hi Niharika, I'm sorry to bother you. my name is Qiqi Guo and I'm a postdoctoral researcher
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could not open file pGe.sjdbGTFfile
Hi Niharika, I'm sorry to bother you. my name is Qiqi Guo and I'm a postdoctoral researcher
Apr 17
chunyu chen
Apr 6
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
unread,
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
Apr 6
larraitz larrañaga
,
Alexander Dobin
2
Mar 20
no output at generating genome indexes
Hi Larraitz, please specify full path to STAR executable. On Thursday, March 16, 2023 at 2:34:35 PM
unread,
no output at generating genome indexes
Hi Larraitz, please specify full path to STAR executable. On Thursday, March 16, 2023 at 2:34:35 PM
Mar 20
Matt K
,
Alexander Dobin
3
Mar 12
Add custom genes to genome without whole new generate genome
That's amazing, thanks for this information. On Wednesday, February 22, 2023 at 11:39:56 AM UTC-5
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Add custom genes to genome without whole new generate genome
That's amazing, thanks for this information. On Wednesday, February 22, 2023 at 11:39:56 AM UTC-5
Mar 12
Assa Yeroslaviz
,
Alexander Dobin
2
Mar 3
segmentation fault when running with --soloType SmartSeq
Hi Assa, --soloType SmartSeq requires specifying cell IDs. It's easiest to do it in the --
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segmentation fault when running with --soloType SmartSeq
Hi Assa, --soloType SmartSeq requires specifying cell IDs. It's easiest to do it in the --
Mar 3
Holger Trucks-Jansen
Mar 2
Segmentation fault (core dumped) during mapping
Hi, I get a Segmentation fault (core dumped) during mapping with starsolo, using star 2.7.10b. Any
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Segmentation fault (core dumped) during mapping
Hi, I get a Segmentation fault (core dumped) during mapping with starsolo, using star 2.7.10b. Any
Mar 2
Ryan Englander
,
Alexander Dobin
2
Feb 28
STAR running endlessly when mapping a sample
Hi Ryan, Which parameters did you map this sample with when it was successful? I would recommend
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STAR running endlessly when mapping a sample
Hi Ryan, Which parameters did you map this sample with when it was successful? I would recommend
Feb 28
Ryan Englander
,
Alexander Dobin
2
Feb 22
Producing sjdbFileChrStartEnd to add noncanonical junctions
Hi Ryan, For unknown strand, you can use . (dot) symbol. Cheers Alex On Saturday, February 11, 2023
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Producing sjdbFileChrStartEnd to add noncanonical junctions
Hi Ryan, For unknown strand, you can use . (dot) symbol. Cheers Alex On Saturday, February 11, 2023
Feb 22
Aggelos Kozonakis
,
Alexander Dobin
3
Feb 6
STAR indexing with gff format
Hi, For the human genome, I recommend using the FASTA and GTF from Gencode or Ensembl. They have
unread,
STAR indexing with gff format
Hi, For the human genome, I recommend using the FASTA and GTF from Gencode or Ensembl. They have
Feb 6
Paul Klein
,
Alexander Dobin
2
Feb 6
Unable to generate STAR index for mouse transcriptome (blocked)
Hi Paul, please switch to the latest version of STAR: https://github.com/alexdobin/STAR/releases/tag/
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Unable to generate STAR index for mouse transcriptome (blocked)
Hi Paul, please switch to the latest version of STAR: https://github.com/alexdobin/STAR/releases/tag/
Feb 6
Matteo Di Bernardo
,
Alexander Dobin
2
Feb 6
Allele specific mapping strategies with STAR
Hi Matteo, I think the no-mismatch requirement is not needed - STAR chooses the best-scoring
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Allele specific mapping strategies with STAR
Hi Matteo, I think the no-mismatch requirement is not needed - STAR chooses the best-scoring
Feb 6
Jose Manuel Latorre Estivalis
, …
Alexander Dobin
6
Feb 3
--outFilterMultimapNmax option
Hi Matteo, You are correct: GeneCounts output always counts only unique mappers - it does not depend
unread,
--outFilterMultimapNmax option
Hi Matteo, You are correct: GeneCounts output always counts only unique mappers - it does not depend
Feb 3
Assa Yeroslaviz
,
Alexander Dobin
2
Feb 3
too many short reads failed to map
Hi Assa, the reads are short to begin with, and the mapped portion of the reads that could map is
unread,
too many short reads failed to map
Hi Assa, the reads are short to begin with, and the mapped portion of the reads that could map is
Feb 3
akhst7
Jan 28
StarSolo with parameters for matching Cell Rager 7.0.x generates an empty mtx file.
HI, I've been trying yo run STARSolo, matching Cell Rager 7.0.x results as follows; #!/bin/bash
unread,
StarSolo with parameters for matching Cell Rager 7.0.x generates an empty mtx file.
HI, I've been trying yo run STARSolo, matching Cell Rager 7.0.x results as follows; #!/bin/bash
Jan 28
Ryan Englander
,
Alexander Dobin
2
Jan 12
twoPassMode --Basic: will junctions inserted on the fly be considered annotated?
Hi Ryan, that's correct; the novel junctions from the 1st pass inserted in the genome for the 2nd
unread,
twoPassMode --Basic: will junctions inserted on the fly be considered annotated?
Hi Ryan, that's correct; the novel junctions from the 1st pass inserted in the genome for the 2nd
Jan 12
Jake W
,
Alexander Dobin
3
Jan 10
Mapping highly repeated sequences
Thank you. I've tried a number of variations of these but have not had any success. I will have
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Mapping highly repeated sequences
Thank you. I've tried a number of variations of these but have not had any success. I will have
Jan 10
Z
,
Alexander Dobin
2
Jan 10
Monkey genome
Hi Z, it seems it could not allocate ~30GB. Please try to increase it (before STAR run) with ulimit -
unread,
Monkey genome
Hi Z, it seems it could not allocate ~30GB. Please try to increase it (before STAR run) with ulimit -
Jan 10
Federico Ansaloni
Jan 9
STARsolo soloMultiMappers cell calling
Hi, I am running STARsolo enabling the counting of multi--gene UMI (--soloMultiMappers EM). I was
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STARsolo soloMultiMappers cell calling
Hi, I am running STARsolo enabling the counting of multi--gene UMI (--soloMultiMappers EM). I was
Jan 9
Hyunhee Hong
2
Jan 4
genomeFastaFile error
Never mind, I solved the problem. Another issue happens, the mapping speed is too slow. Is there any
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genomeFastaFile error
Never mind, I solved the problem. Another issue happens, the mapping speed is too slow. Is there any
Jan 4