Groups
Conversations
All groups and messages
Send feedback to Google
Help
Training
Sign in
Groups
rna-star
Conversations
Labels
About
rna-star
Contact owners and managers
1–30 of 1948
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
Mark all as read
Report abusive group
0 selected
Xiao Lei
,
Alexander Dobin
2
Dec 6
Does STAR aligner need the information from annotation file to identify chimeric reads?
Hi Xiao, Yes, STAR chimeric detection does not use annotations, so you can chimeras between
unread,
Does STAR aligner need the information from annotation file to identify chimeric reads?
Hi Xiao, Yes, STAR chimeric detection does not use annotations, so you can chimeras between
Dec 6
Imchen
,
Alexander Dobin
2
Dec 6
STAR: Use multiple reference genomes at the same time
Hi Imchen, You can generate the combined genome for all the 20 genomes, and map to it, provided that
unread,
STAR: Use multiple reference genomes at the same time
Hi Imchen, You can generate the combined genome for all the 20 genomes, and map to it, provided that
Dec 6
Mario Keller
,
Alexander Dobin
4
Dec 6
--outSJfilterDistToOtherSJmin
Hi Mario, Yes, absolutely - reducing stringency at mapping and more careful post-processing is the
unread,
--outSJfilterDistToOtherSJmin
Hi Mario, Yes, absolutely - reducing stringency at mapping and more careful post-processing is the
Dec 6
Jurgen Moonen
,
Alexander Dobin
2
Dec 6
Paired end sequencing: unmapped too short high
Hi Jurgen, When reads are mapped together, they have to map concordantly - discordant alignments are
unread,
Paired end sequencing: unmapped too short high
Hi Jurgen, When reads are mapped together, they have to map concordantly - discordant alignments are
Dec 6
Lanwu Xiao
Nov 17
A question about multimap
HI Alex, Thanks for helping with STAR relating problems. I'm trying to align a read from one
unread,
A question about multimap
HI Alex, Thanks for helping with STAR relating problems. I'm trying to align a read from one
Nov 17
marie-christine combes
2
Nov 14
STARdiploid
Hi Alexander, For improving of STAR manual, the problem comes from a typing error : F is missing in
unread,
STARdiploid
Hi Alexander, For improving of STAR manual, the problem comes from a typing error : F is missing in
Nov 14
Harry Fischl
,
Alexander Dobin
3
Oct 19
STAR failing to index A to G converted human genome with --sjdbGTFfile
Hi Alex, Thanks for your reply. This still seems to get stuck at the same stage with this --
unread,
STAR failing to index A to G converted human genome with --sjdbGTFfile
Hi Alex, Thanks for your reply. This still seems to get stuck at the same stage with this --
Oct 19
Peter Tam
,
Alexander Dobin
2
Oct 12
Partial or compelte string matches in STAR parameters
Hi Peter, STAR only looks for a complete match. On Thursday, October 12, 2023 at 3:34:39 PM UTC-4
unread,
Partial or compelte string matches in STAR parameters
Hi Peter, STAR only looks for a complete match. On Thursday, October 12, 2023 at 3:34:39 PM UTC-4
Oct 12
Lauren Fletcher
,
Alexander Dobin
2
Oct 12
Low unique maping when aligning smRNA-seq data using STAR
Hi Lauren, in the 1st run, you restricted the number of mismatches to --outFilterMismatchNmax 1 with
unread,
Low unique maping when aligning smRNA-seq data using STAR
Hi Lauren, in the 1st run, you restricted the number of mismatches to --outFilterMismatchNmax 1 with
Oct 12
Stevie Pederson
,
Alexander Dobin
2
Sep 22
STARconsensus: Map reference transcriptome to panhuman reference
Hi Stephen, Are you trying to map full-length transcripts? This would require STARlong, as standard
unread,
STARconsensus: Map reference transcriptome to panhuman reference
Hi Stephen, Are you trying to map full-length transcripts? This would require STARlong, as standard
Sep 22
Shaunak Adkar
,
Alexander Dobin
2
Sep 8
error: could not open input file /geneInfo.tab
Hi Shaunak, did you use GTF file when generating the genome index? On Friday, September 8, 2023 at 7:
unread,
error: could not open input file /geneInfo.tab
Hi Shaunak, did you use GTF file when generating the genome index? On Friday, September 8, 2023 at 7:
Sep 8
Matt K
,
Alexander Dobin
2
Sep 5
Advice on dealing with edited genome
Hi Matt, 1) The endogenous sequence is still present, but not associated with a gtf entry. Will this
unread,
Advice on dealing with edited genome
Hi Matt, 1) The endogenous sequence is still present, but not associated with a gtf entry. Will this
Sep 5
Ezhil A
,
Alexander Dobin
2
Aug 28
Encode miRNA-Seq analysis pipeline - *INPUT FILE* error: could not open input file /geneInfo.tab
Hi Ezhil, please send me the Log.out file. On Monday, August 28, 2023 at 11:16:00 AM UTC-4 ezh...@
unread,
Encode miRNA-Seq analysis pipeline - *INPUT FILE* error: could not open input file /geneInfo.tab
Hi Ezhil, please send me the Log.out file. On Monday, August 28, 2023 at 11:16:00 AM UTC-4 ezh...@
Aug 28
Nikelle Petrillo
, …
Alexander Dobin
5
Aug 28
how to go from --quantMode GeneCounts to DESeq2
Hi, for "reverse"-stranded libraries, the 4th column should be used. On Friday, August 18,
unread,
how to go from --quantMode GeneCounts to DESeq2
Hi, for "reverse"-stranded libraries, the 4th column should be used. On Friday, August 18,
Aug 28
Gen B
Aug 18
Question about using genome annotation for STAR mapping
Hello, I have some questions about using a genome annotation file (.gtf) as input for STAR
unread,
Question about using genome annotation for STAR mapping
Hello, I have some questions about using a genome annotation file (.gtf) as input for STAR
Aug 18
Mayukh Mondal
Aug 9
Subsetting fastq gives different results for cell bar code in STAR solo
Hi, So I have big fastq files generated from BDRhapsody single cell sequences. To make it parallelize
unread,
Subsetting fastq gives different results for cell bar code in STAR solo
Hi, So I have big fastq files generated from BDRhapsody single cell sequences. To make it parallelize
Aug 9
law...@g.harvard.edu
,
Alexander Dobin
2
Jul 20
std::bad_alloc for genomeGenerate
Hi, a good estimate for genome size is ~(9...10)*GenomeLength, so you may need ~250GB of RAM. Another
unread,
std::bad_alloc for genomeGenerate
Hi, a good estimate for genome size is ~(9...10)*GenomeLength, so you may need ~250GB of RAM. Another
Jul 20
Mario Keller
,
Alexander Dobin
2
Jul 19
Chimeric.out.junction and SJ.out.tab
Hi Mario, yes, these rows can be combined. Chimeric.out.junction reports the alignment of Read1 and
unread,
Chimeric.out.junction and SJ.out.tab
Hi Mario, yes, these rows can be combined. Chimeric.out.junction reports the alignment of Read1 and
Jul 19
Jack Engel
,
Alexander Dobin
2
Jul 10
STAR Cigar Strings Not Matching // N-masked genome
Hi Jack, STAR should not have a problem with rare Ns in the genome. Please check that masking Ns did
unread,
STAR Cigar Strings Not Matching // N-masked genome
Hi Jack, STAR should not have a problem with rare Ns in the genome. Please check that masking Ns did
Jul 10
Joshua Mincer
, …
Alexander Dobin
4
Jul 10
STAR --runThreadN benefit plateau?
Simultaneous processes will not conflict if you use distinct --outFileNamePrefix . However, they may
unread,
STAR --runThreadN benefit plateau?
Simultaneous processes will not conflict if you use distinct --outFileNamePrefix . However, they may
Jul 10
Laura García
,
Alexander Dobin
4
Jul 10
Time to build mouse genome index
Hi Laura, if you have 32GB of RAM and 8 threads, it should compete in <2 hours. And you would not
unread,
Time to build mouse genome index
Hi Laura, if you have 32GB of RAM and 8 threads, it should compete in <2 hours. And you would not
Jul 10
Ginger Geiger
,
Alexander Dobin
2
Jun 28
STAR genome map- reads too short
Hi Ginger, my suggestions to figure out why the alignments are "too short": 1. Map read1
unread,
STAR genome map- reads too short
Hi Ginger, my suggestions to figure out why the alignments are "too short": 1. Map read1
Jun 28
Stéphane Pelletier
,
Alexander Dobin
2
Jun 28
star and number of read
Hi Stéphane STAR considers mate1 and mate2 as one paired-end read. On Friday, June 23, 2023 at 8:40:
unread,
star and number of read
Hi Stéphane STAR considers mate1 and mate2 as one paired-end read. On Friday, June 23, 2023 at 8:40:
Jun 28
Yasir Kusay
,
Alexander Dobin
2
Jun 28
Purpose of Parent Transcripts for an Exon
STAR needs to know which exons belong to which transcripts, so that it can extract splice junctions
unread,
Purpose of Parent Transcripts for an Exon
STAR needs to know which exons belong to which transcripts, so that it can extract splice junctions
Jun 28
Arik Harel
,
Alexander Dobin
2
Jun 28
"% of reads mapped to multiple loci" is zero but "% of reads mapped to too many loci" is 17%
Hi, it makes sense since you used --outFilterMultimapNmax 1 This outputs only unique mappers, and all
unread,
"% of reads mapped to multiple loci" is zero but "% of reads mapped to too many loci" is 17%
Hi, it makes sense since you used --outFilterMultimapNmax 1 This outputs only unique mappers, and all
Jun 28
mehwish wahid
,
Alexander Dobin
2
Jun 28
error while Alignment
Hi, it seems like your FASTQ file has empty sequences. If you trimmed the reads, please make sure
unread,
error while Alignment
Hi, it seems like your FASTQ file has empty sequences. If you trimmed the reads, please make sure
Jun 28
Emaan Fatima
,
Alexander Dobin
2
Jun 8
Error in RNA star solo
There is no error message here. Can you find the Log.out file that STAR generated. On Thursday, June
unread,
Error in RNA star solo
There is no error message here. Can you find the Log.out file that STAR generated. On Thursday, June
Jun 8
Darwin Dsouza
,
Alexander Dobin
2
Jun 8
Multimapped hits differences for same reference
Hi Darwin, this is indeed strange. I would recommend adding a few sequences at a time (10100,1000...)
unread,
Multimapped hits differences for same reference
Hi Darwin, this is indeed strange. I would recommend adding a few sequences at a time (10100,1000...)
Jun 8
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
unread,
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