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1–30 of many
Matteo Di Bernardo
,
Alexander Dobin
2
2/6/23
Allele specific mapping strategies with STAR
--
outMultimapperOrder
> Random \ --soloCBwhitelist > whitelist/3_V3.txt \ --soloUMIlen 12 \ --soloCBlen 16 \ --soloUMIstart 17 \ --readFilesCommand > gunzip -c >
unread,
Allele specific mapping strategies with STAR
--
outMultimapperOrder
> Random \ --soloCBwhitelist > whitelist/3_V3.txt \ --soloUMIlen 12 \ --soloCBlen 16 \ --soloUMIstart 17 \ --readFilesCommand > gunzip -c >
2/6/23
Federico Ansaloni
1/9/23
STARsolo soloMultiMappers cell calling
--
outMultimapperOrder
Random --soloType CB_UMI_Simple --soloCBwhitelist $wl --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 8 --soloStrand Forward --soloFeatures
unread,
STARsolo soloMultiMappers cell calling
--
outMultimapperOrder
Random --soloType CB_UMI_Simple --soloCBwhitelist $wl --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 8 --soloStrand Forward --soloFeatures
1/9/23
Rosario Distefano
,
Alexander Dobin
2
11/16/22
Need help validating STAR 2-pass mode with ~50bp RNA-Seq data
--
outMultimapperOrder
Random \ > --seedSearchStartLmax 25 \ > --winAnchorMultimapNmax 100 \ > --outFilterMismatchNoverReadLmax 0.05 \ > --outFilterMatchNminOverLread
unread,
Need help validating STAR 2-pass mode with ~50bp RNA-Seq data
--
outMultimapperOrder
Random \ > --seedSearchStartLmax 25 \ > --winAnchorMultimapNmax 100 \ > --outFilterMismatchNoverReadLmax 0.05 \ > --outFilterMatchNminOverLread
11/16/22
Jason White
,
Alexander Dobin
2
6/7/21
FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem
Hi Alex, All of my star runs are failing alignment with the same error: EXITING because of FATAL ERROR: cannot insert junctions on the fly because of
unread,
FATAL ERROR: cannot insert junctions on the fly because of strand GstrandBit problem
Hi Alex, All of my star runs are failing alignment with the same error: EXITING because of FATAL ERROR: cannot insert junctions on the fly because of
6/7/21
Oladele Oluwayiose
,
Alexander Dobin
2
3/31/21
STAR for Multiple smRNA FastQ Files
--
outMultimapperOrder
Random --runRNGseed 2021 --outSAMmultNmax 1 * will output one alignment per read, for both unique and multi-mapping reads. 3. *--outSAMunmapped Within
unread,
STAR for Multiple smRNA FastQ Files
--
outMultimapperOrder
Random --runRNGseed 2021 --outSAMmultNmax 1 * will output one alignment per read, for both unique and multi-mapping reads. 3. *--outSAMunmapped Within
3/31/21
fantac...@gmail.com
,
Alexander Dobin
2
3/20/21
Same gene sequence but with different mapped reads
--
outMultimapperOrder
Old 2.4` `--
outMultimapperOrder
> Random ` > tRNA-Ala-CGC-1-1 74 37 37 > tRNA-Ala-CGC-1-2 74 3 3 > tRNA-Ala-CGC-1-3 74 3 3 > tRNA-Ala-CGC
unread,
Same gene sequence but with different mapped reads
--
outMultimapperOrder
Old 2.4` `--
outMultimapperOrder
> Random ` > tRNA-Ala-CGC-1-1 74 37 37 > tRNA-Ala-CGC-1-2 74 3 3 > tRNA-Ala-CGC-1-3 74 3 3 > tRNA-Ala-CGC
3/20/21
Lynne Hagelthorn
,
Alexander Dobin
2
1/24/21
Cannot insert sequence on the fly because of strand GstrandBit problem
I'm using STAR for the first time. My lab member gave me a previously used reference genome and gtf. When I try to run it reads Jan 13 19:43:57 ...
unread,
Cannot insert sequence on the fly because of strand GstrandBit problem
I'm using STAR for the first time. My lab member gave me a previously used reference genome and gtf. When I try to run it reads Jan 13 19:43:57 ...
1/24/21
Hartwig Visser
,
Alexander Dobin
2
10/21/20
outMultimapperOrder Default
--
outMultimapperOrder
remains Old_2.4 for now. Cheers Alex On Tuesday, October 20, 2020 at 1:44:52 AM UTC-4, Hartwig Visser wrote: > > Hi All, > > I just wanted to check
unread,
outMultimapperOrder Default
--
outMultimapperOrder
remains Old_2.4 for now. Cheers Alex On Tuesday, October 20, 2020 at 1:44:52 AM UTC-4, Hartwig Visser wrote: > > Hi All, > > I just wanted to check
10/21/20
Hartwig Visser
, …
Alexander Dobin
3
10/14/20
small-RNA seq multi-mapping concerns
--
outMultimapperOrder
Random To consider only top-scoring alignments, you need --outFilterMultimapScoreRange 0 You may also consider increasing --outFilterMultimapNmax
unread,
small-RNA seq multi-mapping concerns
--
outMultimapperOrder
Random To consider only top-scoring alignments, you need --outFilterMultimapScoreRange 0 You may also consider increasing --outFilterMultimapNmax
10/14/20
Andreas
,
Alexander Dobin
2
9/17/20
Reproducibility of alt/ref counts w/STAR alignment (through RSEM)
--
outMultimapperOrder
Random) for each read, but with multithreading, the order of the output reads differs from run to run - which affect RSEM quantifications. The way we solved
unread,
Reproducibility of alt/ref counts w/STAR alignment (through RSEM)
--
outMultimapperOrder
Random) for each read, but with multithreading, the order of the output reads differs from run to run - which affect RSEM quantifications. The way we solved
9/17/20
Luca Stefanucci
,
Alexander Dobin
4
3/9/20
Problem with STAR and fastq format
> >
outMultimapperOrder
Old_2.4 > > outSAMtype SAM > > outSAMmode Full > > outSAMstrandField None > > outSAMattributes Standard > > outSAMunmapped
unread,
Problem with STAR and fastq format
> >
outMultimapperOrder
Old_2.4 > > outSAMtype SAM > > outSAMmode Full > > outSAMstrandField None > > outSAMattributes Standard > > outSAMunmapped
3/9/20
Suraj Kannan
,
Alexander Dobin
4
2/3/20
Including GTF during index generation vs on-the-fly to reduce pseudogene mapping
--
outMultimapperOrder
Random? This is required if primary alignments (--outSAMmultNmax 1) are used for counting because otherwise the primary alignment is not assigned randomly
unread,
Including GTF during index generation vs on-the-fly to reduce pseudogene mapping
--
outMultimapperOrder
Random? This is required if primary alignments (--outSAMmultNmax 1) are used for counting because otherwise the primary alignment is not assigned randomly
2/3/20
Tevfik Kitapci
,
Alexander Dobin
5
7/24/19
Empty bam file
Hi, Apologies if I am doing a double post but I am not sure if github or this forum is more active I asked this question here as well https://github.
unread,
Empty bam file
Hi, Apologies if I am doing a double post but I am not sure if github or this forum is more active I asked this question here as well https://github.
7/24/19
Federico Ansaloni
,
Alexander Dobin
2
7/9/19
different number of mapped reads with/without quantMode
--
outMultimapperOrder
Random --outSAMtype BAM > Unsorted --outStd BAM_Unsorted --runThreadN 20 --genomeDir $wd > --readFilesIn $reads --readFilesCommand zcat >
unread,
different number of mapped reads with/without quantMode
--
outMultimapperOrder
Random --outSAMtype BAM > Unsorted --outStd BAM_Unsorted --runThreadN 20 --genomeDir $wd > --readFilesIn $reads --readFilesCommand zcat >
7/9/19
Joseph Mudd
, …
Alexander Dobin
3
4/22/19
multi-mappers (non-ribosomal)
Hi Alex, In one of my runs I'm getting a near ~50% of multi-mappers (attached log.final.out). I thought these may be ribosomal. However I've
unread,
multi-mappers (non-ribosomal)
Hi Alex, In one of my runs I'm getting a near ~50% of multi-mappers (attached log.final.out). I thought these may be ribosomal. However I've
4/22/19
Joseph Mudd
,
Alexander Dobin
2
4/11/19
stuck at ...started mapping
Hi Alex, I have a run that is stalled at the mapping stage. I'm needing some advice because the day before, I successfully completed a similar run
unread,
stuck at ...started mapping
Hi Alex, I have a run that is stalled at the mapping stage. I'm needing some advice because the day before, I successfully completed a similar run
4/11/19
Pierre-emmanuel Bonté
,
Alexander Dobin
5
3/21/19
Issue with chimeric junctions mapping SMART-seq2 reads
--
outMultimapperOrder
Random \ >> --outFilterMismatchNoverLmax 0.04 \ >> --outFilterMatchNminOverLread 0.33 \ >> --outFilterScoreMinOverLread 0.33
unread,
Issue with chimeric junctions mapping SMART-seq2 reads
--
outMultimapperOrder
Random \ >> --outFilterMismatchNoverLmax 0.04 \ >> --outFilterMatchNminOverLread 0.33 \ >> --outFilterScoreMinOverLread 0.33
3/21/19
Diego
2
3/12/19
Discordant reads in STAR output
--
outMultimapperOrder
Random --outSAMprimaryFlag AllBestScore >> --outSAMstrandField intronMotif --runRNGseed 23 --outSAMtype BAM Unsorted >> --quantMode
unread,
Discordant reads in STAR output
--
outMultimapperOrder
Random --outSAMprimaryFlag AllBestScore >> --outSAMstrandField intronMotif --runRNGseed 23 --outSAMtype BAM Unsorted >> --quantMode
3/12/19
Alex Chitsazan
, …
Alexander Dobin
7
2/1/19
Is STAR deterministic?
--
outMultimapperOrder
Old_2.4, if you want it random, you would need >> --
outMultimapperOrder
Random >> >> Cheers >> Alex >> >> On Wednesday
unread,
Is STAR deterministic?
--
outMultimapperOrder
Old_2.4, if you want it random, you would need >> --
outMultimapperOrder
Random >> >> Cheers >> Alex >> >> On Wednesday
2/1/19
Stefano
,
Alexander Dobin
4
1/29/19
Problem during genome loading
>>
outMultimapperOrder
Old_2.4 >> outSAMtype SAM >> outSAMmode Full >> outSAMstrandField None >> outSAMattributes Standard >> outSAMunmapped
unread,
Problem during genome loading
>>
outMultimapperOrder
Old_2.4 >> outSAMtype SAM >> outSAMmode Full >> outSAMstrandField None >> outSAMattributes Standard >> outSAMunmapped
1/29/19
Josh Espinoza
,
Alexander Dobin
2
1/24/19
STAR aligner is stuck after "Finished loading and checking parameters" in "Log.out"
0 >
outMultimapperOrder
Old_2.4 > outSAMtype SAM > outSAMmode Full > outSAMstrandField None > outSAMattributes Standard > outSAMunmapped None > outSAMorder
unread,
STAR aligner is stuck after "Finished loading and checking parameters" in "Log.out"
0 >
outMultimapperOrder
Old_2.4 > outSAMtype SAM > outSAMmode Full > outSAMstrandField None > outSAMattributes Standard > outSAMunmapped None > outSAMorder
1/24/19
Yong Liu
,
Alexander Dobin
4
10/30/18
single cell RNA seq mapping issue to pig genome by cellranger2.20 which wrapped STAR
>>
outMultimapperOrder
Old_2.4 >>> outSAMtype SAM >>> outSAMmode Full >>> outSAMstrandField None >>> outSAMattributes Standard
unread,
single cell RNA seq mapping issue to pig genome by cellranger2.20 which wrapped STAR
>>
outMultimapperOrder
Old_2.4 >>> outSAMtype SAM >>> outSAMmode Full >>> outSAMstrandField None >>> outSAMattributes Standard
10/30/18
salim...@gmail.com
,
Ramakrishnan
2
10/6/18
STAR mapping issue
Hi all, I am trying to run STAR on some sample on a server and while it seems to run just fine I am facing 2 issues which I actually think is only one.
unread,
STAR mapping issue
Hi all, I am trying to run STAR on some sample on a server and while it seems to run just fine I am facing 2 issues which I actually think is only one.
10/6/18
Rez
,
Alexander Dobin
3
8/16/18
Issues with processing annotations
--
outMultimapperOrder
Random --outFilterMultimapNmax 1 \ >> --readFilesCommand zcat \ >> --readFilesIn condition_paired_1.fq.gz condition_paired_2.fq.gz
unread,
Issues with processing annotations
--
outMultimapperOrder
Random --outFilterMultimapNmax 1 \ >> --readFilesCommand zcat \ >> --readFilesIn condition_paired_1.fq.gz condition_paired_2.fq.gz
8/16/18
Federico Ansaloni
,
Alexander Dobin
6
7/13/18
max mismatch parameter issue
--
outMultimapperOrder
Random >>>>> --outSAMtype BAM Unsorted --outSAMunmapped None >>>>> --outSAMprimaryFlag AllBestScore --outFilterMismat
unread,
max mismatch parameter issue
--
outMultimapperOrder
Random >>>>> --outSAMtype BAM Unsorted --outSAMunmapped None >>>>> --outSAMprimaryFlag AllBestScore --outFilterMismat
7/13/18
Federico Ansaloni
,
Brett Vanderwerff
3
8/19/18
segmentation fault
--
outMultimapperOrder
Random --outStd SAM --runThreadN 20 --genomeDir $wd --readFilesIn $reads1 $reads2 > Aligned.sam If I create the index and then analyze just one sample
unread,
segmentation fault
--
outMultimapperOrder
Random --outStd SAM --runThreadN 20 --genomeDir $wd --readFilesIn $reads1 $reads2 > Aligned.sam If I create the index and then analyze just one sample
8/19/18
Nicolás Lemus
,
Alexander Dobin
2
6/7/18
Can get bedGrahp from STAR
0 >
outMultimapperOrder
Old_2.4 > outSAMtype SAM > outSAMmode Full > outSAMstrandField None > outSAMattributes Standard > outSAMunmapped None > outSAMorder
unread,
Can get bedGrahp from STAR
0 >
outMultimapperOrder
Old_2.4 > outSAMtype SAM > outSAMmode Full > outSAMstrandField None > outSAMattributes Standard > outSAMunmapped None > outSAMorder
6/7/18
praful aggarwal
, …
Ralf C. Mueller
48
3/31/20
STAR for miRNA
--
outMultimapperOrder
Random) with featureCounts --primary option. If you want a more comprehesive accounting for multimappers, you would have to build a custom pipeline for this
unread,
STAR for miRNA
--
outMultimapperOrder
Random) with featureCounts --primary option. If you want a more comprehesive accounting for multimappers, you would have to build a custom pipeline for this
3/31/20
Vempalli Fazulur
,
Alexander Dobin
9
4/21/18
STAR - high number of reads mapped to multiple loci
> -
outMultimapperOrder
option. >>>> >>>> Thanks & Regards >>>> Fazulur Rehaman >>>> >>>> On Monday
unread,
STAR - high number of reads mapped to multiple loci
> -
outMultimapperOrder
option. >>>> >>>> Thanks & Regards >>>> Fazulur Rehaman >>>> >>>> On Monday
4/21/18
Jacob Musser
,
Alexander Dobin
2
3/9/18
question about mapping multiple samples
--
outMultimapperOrder
Random > --genomeDir /star_genome_index_gtf/ --sjdbGTFfile > /star_genome_index_gtf/Trichoplax_scaffolds_JGI_AUGUSTUS_maxtrack2.gtf
unread,
question about mapping multiple samples
--
outMultimapperOrder
Random > --genomeDir /star_genome_index_gtf/ --sjdbGTFfile > /star_genome_index_gtf/Trichoplax_scaffolds_JGI_AUGUSTUS_maxtrack2.gtf
3/9/18