Groups
Conversations
All groups and messages
Send feedback to Google
Help
Sign in
Groups
rna-star
Conversations
Labels
About
rna-star
1–30 of 1875
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
HelenK.
,
Alexander Dobin
2
Jul 12
Missing reads after STAR alignment: present in FASTQ; missing from output.bam and unmapped.out.mate files
Hi Helen, bu default STAR does not output unmapped alignments, if you need it, please add this option
unread,
Missing reads after STAR alignment: present in FASTQ; missing from output.bam and unmapped.out.mate files
Hi Helen, bu default STAR does not output unmapped alignments, if you need it, please add this option
Jul 12
Babak A
,
Alexander Dobin
3
Jul 12
FATAL ERROR when using --parameterFiles
Hi Babak, sorry for the delayed reply. Yes, that correct - the double dashes are only used on the
unread,
FATAL ERROR when using --parameterFiles
Hi Babak, sorry for the delayed reply. Yes, that correct - the double dashes are only used on the
Jul 12
Maoting Chen
,
Alexander Dobin
4
Jul 12
STAR mapping and HTSeq for stranded RNA-seq
Hi Maoting, sorry for the belayed reply. Concatenating junctions from all samples will increase
unread,
STAR mapping and HTSeq for stranded RNA-seq
Hi Maoting, sorry for the belayed reply. Concatenating junctions from all samples will increase
Jul 12
jacs
,
Alexander Dobin
4
Jun 10
STAR alignment , remove duplicate, RSEM
Hi Jacs, what you are doing on STAR side is correct. This is RSEM error: fail to open file '
unread,
STAR alignment , remove duplicate, RSEM
Hi Jacs, what you are doing on STAR side is correct. This is RSEM error: fail to open file '
Jun 10
Dario Strbenac
Jun 7
Suitable Parameters for Intronic Retrotransposon Splicing
A recent journal article found an unusual variety of splicing where an exon of a known gene is
unread,
Suitable Parameters for Intronic Retrotransposon Splicing
A recent journal article found an unusual variety of splicing where an exon of a known gene is
Jun 7
Alexander Dobin
, …
Ahmed Gamal
23
Jun 6
new release: counting reads per gene
Hi Dario, My issue is that I get about 5-6 times more ambiguous reads than the counted ones. So, I
unread,
new release: counting reads per gene
Hi Dario, My issue is that I get about 5-6 times more ambiguous reads than the counted ones. So, I
Jun 6
Babak A
,
Alexander Dobin
5
Jun 1
Mapping short reads
Thanks, Alex! This is indeed helpful. Babak On Wednesday, June 1, 2022 at 10:46:56 AM UTC-7 ado...@
unread,
Mapping short reads
Thanks, Alex! This is indeed helpful. Babak On Wednesday, June 1, 2022 at 10:46:56 AM UTC-7 ado...@
Jun 1
Kelly H
,
Alexander Dobin
3
May 19
Decrease in number of multimapping reads after increasing outFilterMultimapNmax and winAnchorMultimapNmax
Hi Alex, Here are the files, Default has the standard cutoff of 10, and in 200Cutoff I set both
unread,
Decrease in number of multimapping reads after increasing outFilterMultimapNmax and winAnchorMultimapNmax
Hi Alex, Here are the files, Default has the standard cutoff of 10, and in 200Cutoff I set both
May 19
Pia
,
Alexander Dobin
2
May 13
Question about paired-end alignment
Hi Pia, by default, STAR does not output such "chimeric" alignments. You would need to
unread,
Question about paired-end alignment
Hi Pia, by default, STAR does not output such "chimeric" alignments. You would need to
May 13
kyoungmin Lee
,
Alexander Dobin
2
May 13
What's the difference about SJ.out.tab files?
Hi, it seems multiple jobs were run from the same directory. The SRR12345678__SJ.out.tab files was
unread,
What's the difference about SJ.out.tab files?
Hi, it seems multiple jobs were run from the same directory. The SRR12345678__SJ.out.tab files was
May 13
Nathanael Walker-Hale
,
Alexander Dobin
2
May 13
Large difference in mismatch rate per base between samples from the same experiment
Hi Nathanael, A higher mismatch error rate could indicate poorer sequencing quality or library prep
unread,
Large difference in mismatch rate per base between samples from the same experiment
Hi Nathanael, A higher mismatch error rate could indicate poorer sequencing quality or library prep
May 13
Assa Yeroslaviz
,
Alexander Dobin
2
May 2
Mapping Ribo-Seq and mRNA-Seq from the same project
Hi Assa, sorry for the delayed reply. with a highly variable read length for ribo-seq, it's hard
unread,
Mapping Ribo-Seq and mRNA-Seq from the same project
Hi Assa, sorry for the delayed reply. with a highly variable read length for ribo-seq, it's hard
May 2
Sebastián Contreras
,
Alexander Dobin
2
May 2
too low unique reads aligned using paired end data
Hi Sebastian, sorry for the delayed reply. this is likely caused by some inconsistency in the read
unread,
too low unique reads aligned using paired end data
Hi Sebastian, sorry for the delayed reply. this is likely caused by some inconsistency in the read
May 2
Mengjia Fu
,
Alexander Dobin
2
May 2
Question
Hi, I am not familiar with this technology, so cannot really comment on what the acceptable mapped %
unread,
Question
Hi, I am not familiar with this technology, so cannot really comment on what the acceptable mapped %
May 2
Justin
,
Alexander Dobin
2
May 2
Issue with my alignment or poor small RNA-seq dataset?
Hi Justin, sorry for the belayed reply. For small RNA-seq, it's important to trim the adapter,
unread,
Issue with my alignment or poor small RNA-seq dataset?
Hi Justin, sorry for the belayed reply. For small RNA-seq, it's important to trim the adapter,
May 2
Parnika Mukherjee
,
Alexander Dobin
2
Feb 20
Segmentation fault at "processing annotations GTF" step in STAR 2.7.0a
Hi Parnika, 2.7.0a is a very old version, please switch to one of the latest ones, no earlier than
unread,
Segmentation fault at "processing annotations GTF" step in STAR 2.7.0a
Hi Parnika, 2.7.0a is a very old version, please switch to one of the latest ones, no earlier than
Feb 20
Jose Manuel Latorre Estivalis
,
Alexander Dobin
4
Feb 8
--outFilterMultimapNmax option
Hi Jose, yes, presently GeneCounts option counts only uniquely mapping reads, without regard to the -
unread,
--outFilterMultimapNmax option
Hi Jose, yes, presently GeneCounts option counts only uniquely mapping reads, without regard to the -
Feb 8
Labrousse Guillaume
,
Alexander Dobin
2
Feb 7
Process killed
Hi, this looks like RAM problem. Please try --limitGenomeGenerateRAM 25000000000 Cheers Alex On
unread,
Process killed
Hi, this looks like RAM problem. Please try --limitGenomeGenerateRAM 25000000000 Cheers Alex On
Feb 7
Jan Pieter Vanwelkenhuyzen
,
Alexander Dobin
4
Feb 7
Optimal detection of known splice variants
Hi Jan, if you are creating a fast with sequences for all splices, the 2nd alignment pass will likely
unread,
Optimal detection of known splice variants
Hi Jan, if you are creating a fast with sequences for all splices, the 2nd alignment pass will likely
Feb 7
Analeigh Gui
,
Alexander Dobin
2
Feb 1
cannot insert junctions on the fly because of strand GstrandBit problem
Hi Yujuan, please try to add this parameter: --limitSjdbInsertNsj 100 Cheers Alex On Tuesday, January
unread,
cannot insert junctions on the fly because of strand GstrandBit problem
Hi Yujuan, please try to add this parameter: --limitSjdbInsertNsj 100 Cheers Alex On Tuesday, January
Feb 1
Anthony Tercero
,
Alexander Dobin
4
Jan 13
Fatal error when running for-loop to align multiple reads to single indexed genome
Hi Anthony, if you need to map 3 separate experiments, you would need to run STAR 3 times. In each
unread,
Fatal error when running for-loop to align multiple reads to single indexed genome
Hi Anthony, if you need to map 3 separate experiments, you would need to run STAR 3 times. In each
Jan 13
Tonya Brunetti
,
Alexander Dobin
4
12/27/21
Conflicting novel vs annotated junctions in 2-pass mode
Hi Tonya, right, for "true" annotated (iepresent in GTF) comparison, you would ignore the
unread,
Conflicting novel vs annotated junctions in 2-pass mode
Hi Tonya, right, for "true" annotated (iepresent in GTF) comparison, you would ignore the
12/27/21
Raquel F.
,
Alexander Dobin
4
12/27/21
STARsolo 2.7.9a segmentation fault (single-end reads, Smartseq)
Hi Raquel, I forgot about this workaround... :) Thanks! Alex On Monday, December 27, 2021 at 2:20:39
unread,
STARsolo 2.7.9a segmentation fault (single-end reads, Smartseq)
Hi Raquel, I forgot about this workaround... :) Thanks! Alex On Monday, December 27, 2021 at 2:20:39
12/27/21
Daniel Fulop
,
Alexander Dobin
2
12/27/21
Keep orphan read mappings in transcriptome BAM
Hi Dan, you are right, the alignments whose mates are concordant with different genes cannot be
unread,
Keep orphan read mappings in transcriptome BAM
Hi Dan, you are right, the alignments whose mates are concordant with different genes cannot be
12/27/21
Prachiti Prabhu
,
Alexander Dobin
3
12/21/21
Discordant reads output
Thank you, Alex. I appreciate you taking the time to reply. I will try that out and get back to you
unread,
Discordant reads output
Thank you, Alex. I appreciate you taking the time to reply. I will try that out and get back to you
12/21/21
Florencia Mascardi
12/18/21
Discrepancies when analyzing same sample with same FASTA but different methods
Hi Alex, I'm currently trying to analyze whole RNA-sequencing data to reach to the identification
unread,
Discrepancies when analyzing same sample with same FASTA but different methods
Hi Alex, I'm currently trying to analyze whole RNA-sequencing data to reach to the identification
12/18/21
Shraddha Ranganathan
,
Alexander Dobin
3
12/15/21
Using GeneCounts in DESeq2
Hi Alex, Makes sense, thanks for the response! That works just right On Friday, 3 December 2021 at 20
unread,
Using GeneCounts in DESeq2
Hi Alex, Makes sense, thanks for the response! That works just right On Friday, 3 December 2021 at 20
12/15/21
Γεωργία Γιωτοπούλου
,
Alexander Dobin
2
12/3/21
star alignment FVB mouse reference genome
Hi Georgia, what are the mapping stats in the Log.final.out? If the mapping rate is not too low and
unread,
star alignment FVB mouse reference genome
Hi Georgia, what are the mapping stats in the Log.final.out? If the mapping rate is not too low and
12/3/21
Andrei Rozanski
,
Alexander Dobin
3
11/15/21
2-pass mapping - genome annotation of non model organism
Dear Alex, Thanks a lot for the reply. I will proceed with 2nd pass. All the best, AndreiR On
unread,
2-pass mapping - genome annotation of non model organism
Dear Alex, Thanks a lot for the reply. I will proceed with 2nd pass. All the best, AndreiR On
11/15/21
Kohta Ikegami
,
Alexander Dobin
2
11/12/21
Signal.UniqueMultiple vs Signal.Unique bedGraphs
Hi Kohta, you are correct on all points. The reads-per-base counts by default are normalized to RPM,
unread,
Signal.UniqueMultiple vs Signal.Unique bedGraphs
Hi Kohta, you are correct on all points. The reads-per-base counts by default are normalized to RPM,
11/12/21