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/alexdobin/STAR for details.

Most stable release: https://github.com/alexdobin/STAR/releases/tag/2.7.6a

Most recent release: https://github.com/alexdobin/STAR/releases/tag/2.7.8a

0 selected

HelenK., Alexander Dobin2

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

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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 Dobin3

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

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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 Dobin4

Jul 12

STAR mapping and HTSeq for stranded RNA-seq

Hi Maoting, sorry for the belayed reply. Concatenating junctions from all samples will increase

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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 Dobin4

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 '

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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

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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 Gamal23

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

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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 Dobin5

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...@

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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 Dobin3

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

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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 Dobin2

May 13

Question about paired-end alignment

Hi Pia, by default, STAR does not output such "chimeric" alignments. You would need to

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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 Dobin2

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

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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 Dobin2

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

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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 Dobin2

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

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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 Dobin2

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

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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 Dobin2

May 2

Question

Hi, I am not familiar with this technology, so cannot really comment on what the acceptable mapped %

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Question

Hi, I am not familiar with this technology, so cannot really comment on what the acceptable mapped %

May 2

Justin, Alexander Dobin2

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,

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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 Dobin2

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

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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 Dobin4

Feb 8

--outFilterMultimapNmax option

Hi Jose, yes, presently GeneCounts option counts only uniquely mapping reads, without regard to the -

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--outFilterMultimapNmax option

Hi Jose, yes, presently GeneCounts option counts only uniquely mapping reads, without regard to the -

Feb 8

Labrousse Guillaume, Alexander Dobin2

Feb 7

Process killed

Hi, this looks like RAM problem. Please try --limitGenomeGenerateRAM 25000000000 Cheers Alex On

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Process killed

Hi, this looks like RAM problem. Please try --limitGenomeGenerateRAM 25000000000 Cheers Alex On

Feb 7

Jan Pieter Vanwelkenhuyzen, Alexander Dobin4

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

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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 Dobin2

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

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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 Dobin4

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

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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 Dobin4

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

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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 Dobin4

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

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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 Dobin2

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

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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 Dobin3

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

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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

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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 Dobin3

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

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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 Dobin2

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

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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 Dobin3

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

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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 Dobin2

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,

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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