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1–11 of 1964
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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Alexandria Pinto
,
Alexander Dobin
2
7/22/20
Log.final.out for --quantMode TranscriptomeSAM
Hi Alexandria, there is no statistics output for transcriptomic output - that's a great
unread,
STAR
Log.final.out for --quantMode TranscriptomeSAM
Hi Alexandria, there is no statistics output for transcriptomic output - that's a great
7/22/20
Pawan Chinari
,
Alexander Dobin
6
7/22/20
Merging unmapped reads
Hi Pawan, we can store unmapped reads in BAM so that we can have *all* of the reads in the BAM file,
unread,
STAR
fastq
unmapped
Merging unmapped reads
Hi Pawan, we can store unmapped reads in BAM so that we can have *all* of the reads in the BAM file,
7/22/20
Alexandria Pinto
,
Alexander Dobin
2
6/24/20
What is the significance of sjdbOverhang when generating a genome?
Hi Alexandria, the --sjdbOverhang value should have marginal effect on the alignments. You can check
unread,
STAR
rna-seq
What is the significance of sjdbOverhang when generating a genome?
Hi Alexandria, the --sjdbOverhang value should have marginal effect on the alignments. You can check
6/24/20
Eric Londin
,
Alexander Dobin
7
5/8/20
sequence that should map, but doesn't
Thanks, that makes sense to me. The read does in fact map as expected in the first pass, I'm
unread,
STAR
sequence that should map, but doesn't
Thanks, that makes sense to me. The read does in fact map as expected in the first pass, I'm
5/8/20
Vasily A.
,
Alexander Dobin
3
3/9/20
read IDs in the Unmapped.out.mate1/2 files
Thank you for the explanation! (maybe it would also worth to add this info to the manual) On Monday,
unread,
STAR
unmapped
read IDs in the Unmapped.out.mate1/2 files
Thank you for the explanation! (maybe it would also worth to add this info to the manual) On Monday,
3/9/20
Vasily A.
,
Alexander Dobin
2
3/3/20
is STAR MPI-capable?
Hi Vasily, STAR is not MPI-capable, it's only multithreaded on a shared memory system (ie
unread,
MPI
STAR
multithreading
is STAR MPI-capable?
Hi Vasily, STAR is not MPI-capable, it's only multithreaded on a shared memory system (ie
3/3/20
Eric Londin
,
Alexander Dobin
2
2/26/20
Soft-clippings in mapping
Hi Eric, --alignEndsType EndToEnd should disallow all soft-clipping. Please send me the Log.out file
unread,
STAR
Soft-clippings in mapping
Hi Eric, --alignEndsType EndToEnd should disallow all soft-clipping. Please send me the Log.out file
2/26/20
yang chen
,
Alexander Dobin
5
11/25/19
STAR Build genome index using repeat genome (exceeded memory limit (123675052 > 122880000))
Great. Thanks Alex. I will follow your suggestions. Best regards, Yang Chen 在 2019年11月23日星期六 UTC-5上午
unread,
STAR
memory
repeat
STAR Build genome index using repeat genome (exceeded memory limit (123675052 > 122880000))
Great. Thanks Alex. I will follow your suggestions. Best regards, Yang Chen 在 2019年11月23日星期六 UTC-5上午
11/25/19
User_new
,
Alexander Dobin
2
10/19/19
Chimeric.out.junction file issues in segment 2 co-ordinates
Hi @User_new col 5 (eg 1971) is the last base of the intron of the chimeric junction, so the second
unread,
Chimeric
STAR
Chimeric.out.junction file issues in segment 2 co-ordinates
Hi @User_new col 5 (eg 1971) is the last base of the intron of the chimeric junction, so the second
10/19/19
Aditya Saxena
,
Alexander Dobin
2
10/11/19
No GeneCount and bam outputs-STAR2.52a
Hi Aditya, --outSAMtype: command not found. means that you split your command line into two lines,
unread,
STAR
issue
problem
No GeneCount and bam outputs-STAR2.52a
Hi Aditya, --outSAMtype: command not found. means that you split your command line into two lines,
10/11/19
Rajesh Detroja
, …
Alexander Dobin
16
9/24/21
STAR mapping pipeline with 2-pass for multiple samples
Hi Bekah, in general, non-canonical junctions have a much higher rate of false positives, and so
unread,
STAR
STAR mapping pipeline with 2-pass for multiple samples
Hi Bekah, in general, non-canonical junctions have a much higher rate of false positives, and so
9/24/21