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145 results • Page
1 of 3
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Filtering for tag:
salmon
•
reset
0
votes
4
replies
180
views
Help with salmon quantification of samples with de novo transcriptome
salmon
denovo
tximport
updated 4 days ago by
ponganta
▴ 170 • written 6 days ago by
codyas
• 0
0
votes
2
replies
105
views
Inter-species RNAseq normalisation
EdgeR
Deseq2
RNA-Seq
Expression
Salmon
5 weeks ago by
pprice3
• 0
0
votes
6
replies
179
views
What are the best quantification tools for miRNA seq?
miRNA
RNA-Seq
Salmon
miRNA-seq
6 weeks ago by
cecilomar6
• 0
4
votes
7
replies
196
views
Mapping rate troubles
RNA-Seq
alignment
salmon
STAR
SEQmonk
7 weeks ago by
thomas58
▴ 20
4
votes
12
replies
300
views
Salmon BAM target length different to FASTA file sequence length
salmon
Salmon
RNA-Seq
9 weeks ago by
bdy8
▴ 50
4
votes
6
replies
268
views
RNA-Seq Data analysis
RNA-Seq
FPKM
.tsv
Salmon
volcano plots
updated 11 weeks ago by
dsull
★ 1.8k • written 11 weeks ago by
sujitsilas
• 0
5
votes
5
replies
272
views
Batch-correction on tximport data from salmon
salmon
sva
combat
RNA-Seq
DESeq2
4 months ago by
mfrech6
• 0
7
votes
7
replies
385
views
3' RNA-seq (Lexogen Quant-seq) Mapping Problems with Salmon
RNA-Seq
salmon
index
quant
5 months ago by
bdy8
▴ 50
0
votes
0
replies
224
views
How represent isoforms in different tracks in a genome browser?
RNA-Seq
Isoform
reads
alignment
Salmon
updated 5 months ago by
Biostar
20 • written 6 months ago by
Bardt9
• 0
0
votes
6
replies
273
views
Makes sense to conduct SALMON mapping followed by NOIseq for differential expression analysis?
RNA-Seq
SALMON
NOIseq
6 months ago by
YEODYNASTY
▴ 10
0
votes
1
reply
446
views
running salmon on bam files
salmon
STAR
collate
updated 6 months ago by
GenoMax
99k • written 6 months ago by
inah
• 0
0
votes
0
replies
203
views
Using Salmon to Quantify shRNA Library
Salmon
shRNA
6 months ago by
DeadlyFall
• 0
1
vote
1
reply
243
views
CAST/EiJ mouse strain Reference Transcriptome (do we have one? if not, how to build?)
Transcriptome
CAST
mouse
salmon
updated 6 months ago by
mark.ziemann
★ 1.3k • written 6 months ago by
Rhodnius
• 0
1
vote
7
replies
584
views
GTF based salmon index file for GRCh38
RNA-Seq
Salmon
index
6 months ago by
parvathi.sudha
▴ 20
8
votes
9
replies
1.1k
views
6 follow
Building Salmon Index
index
salmon
rna-seq
updated 18 days ago by
jared.andrews07
9.2k • written 6 months ago by
SeroroO
▴ 20
2
votes
2
replies
491
views
Gibbs sampling/bootstrap replicates in Salmon
salmon
uncertainty
updated 6 months ago by
Rob
4.6k • written 6 months ago by
Dunois
▴ 620
0
votes
17
replies
340
views
Transcripts with no read support
RNA-Seq
alignment
assembly
salmon
7 months ago by
Dunois
▴ 620
13
votes
6
replies
1.2k
views
How does salmon deal with decoy?
salmon
rna
RNA-Seq
updated 7 months ago by
Rob
4.6k • written 7 months ago by
Cindy
▴ 10
2
votes
3
replies
379
views
Trouble with choosing the right reference transcriptome file for mm10
RNA-Seq
genome
salmon
kallisto
sequencing
8 months ago by
wyoo083
• 0
2
votes
2
replies
458
views
Salmon with Sleuth
RNA-Seq
Salmon
Sleuth
updated 8 months ago by
dsull
★ 1.8k • written 8 months ago by
koaeb
▴ 10
1
vote
0
replies
274
views
Import Salmon output by tximport
RNA-Seq
R
tximport
salmon
updated 8 months ago by
Ram
32k • written 8 months ago by
koaeb
▴ 10
0
votes
0
replies
307
views
Salmon number of burn-in fragments warning
salmon
RNA-Seq
mapping
updated 8 months ago by
h.mon
32k • written 8 months ago by
bioinfo_cat
• 0
3
votes
2
replies
1.2k
views
Dependencies auto-installed with Conda?
conda
nesoni
salmon
updated 8 months ago by
Biostar
20 • written 4.3 years ago by
Liflock
• 0
1
vote
5
replies
363
views
Tximport error with Salmon data
RNA-Seq
Salmon
R
updated 8 months ago by
Ram
32k • written 8 months ago by
lilyolmstead
• 0
3
votes
2
replies
376
views
Salmon auxiliary output
Salmon
updated 9 months ago by
mcsimenc
▴ 10 • written 18 months ago by
g.wang2
▴ 10
0
votes
6
replies
2.7k
views
Error with snakemake
snakemake
python
pipeline
salmon
updated 9 months ago by
Biostar
20 • written 2.8 years ago by
Biologist
▴ 200
1
vote
0
replies
265
views
Event- vs transcript-based approaches for analyzing alternative splicing
RNA-Seq
alternative splicing
rMATS
Salmon
9 months ago by
fmerkal
▴ 30
8
votes
11
replies
483
views
Transcript level counts from full length scRNA data
scRNA
RNA-Seq
salmon
star
9 months ago by
GouthamAtla
11k
3
votes
8
replies
559
views
Having trouble running Salmon in Anaconda prompt
software error
anaconda
Salmon
python
updated 9 months ago by
zx8754
10k • written 11 months ago by
zal4002
• 0
3
votes
4
replies
285
views
Tximport Error ... unable to match up my quant.sf and tx2gene columns
RNA-Seq
Tximport
salmon
10 months ago by
2405592M
▴ 100
0
votes
3
replies
431
views
Compare expression level of isoforms among conditions - TPM or deseq2 normalised counts?
RNA-Seq
deseq2
tximport
salmon
10 months ago by
tianshenbio
▴ 90
7
votes
21
replies
825
views
DEseq2 results differs greatly when comparing output from STAR/featureCounts and Salmon
RNA-Seq
DEseq2
salmon
STAR
updated 10 months ago by
Rob
4.6k • written 10 months ago by
testtube
▴ 20
0
votes
1
reply
272
views
Salmon validating best settings for use case
salmon
RNA-Seq
validation
11 months ago by
yryan
• 0
0
votes
4
replies
326
views
salmon TPM output to linear regression in R
RNA-Seq
salmon
lm
11 months ago by
evelyn
▴ 140
1
vote
1
reply
451
views
salmon shell script to automate quant
shellscript
salmon
updated 11 months ago by
ATpoint
47k • written 11 months ago by
amitpande74
▴ 20
25
votes
15
replies
4.1k
views
6 follow
Mapping vs Quasi-Mapping
salmon
quasi-mapping
updated 11 months ago by
biochemistry-tehran
• 0 • written 2.7 years ago by
pablo
▴ 160
1
vote
2
replies
236
views
Can you use salmon bootstraps to increase sample size for machine learning
RNA-Seq
salmon
machine learning
updated 11 months ago by
ATpoint
47k • written 11 months ago by
yryan
• 0
9
votes
3
replies
610
views
Salmon: Any downstream DEA tools which uses abundance estimate variation information?
salmon
deseq2
updated 11 months ago by
ATpoint
47k • written 2.2 years ago by
Thomas
▴ 100
0
votes
1
reply
909
views
Help with Salmon --> tximport --> edgeR
RNA-Seq
tximport
salmon
edgeR
normalisation
11 months ago by
u3005992
▴ 20
3
votes
3
replies
434
views
Salmon only processes human reads from PDX data
salmon
RNA-Seq
alignment
software error
updated 11 months ago by
sandeep.amberkar18
▴ 50 • written 14 months ago by
jrleary
▴ 170
2
votes
3
replies
1.5k
views
featureCounts with pseudobam
RNA-Seq
pseudobam
featureCounts
kallisto
Salmon
updated 12 months ago by
ATpoint
47k • written 4.2 years ago by
mccormack
▴ 70
1
vote
6
replies
413
views
What causes strange oscillations in the count distribution of Salmon and STAR aligned gene tables?
salmon
STAR
counts
filtering
HTSeq
12 months ago by
Gabriel
▴ 90
6
votes
1
reply
499
views
From transcript to gene - Salmon quantification
Salmon
updated 13 months ago by
ATpoint
47k • written 13 months ago by
JulianC
▴ 10
1
vote
1
reply
261
views
quantify tRNA-derived fragments on RNA-seq data
RNA-Seq
tRNA-derived fragments
Salmon
13 months ago by
lkianmehr
▴ 50
6
votes
6
replies
473
views
Salmon annotation of transcripts in quasi-mapping step
salmon
pseudoalignment
mapping
13 months ago by
Iara Souza
• 0
6
votes
10
replies
328
views
can salmon distinguish similar transcript?
RNA-Seq
salmon
updated 13 months ago by
ATpoint
47k • written 13 months ago by
arezu.lari
• 0
2
votes
7
replies
320
views
MPI/multi-threading in salmon quasi-mapping
salmon
RNA-Seq
updated 13 months ago by
Devon Ryan
98k • written 13 months ago by
vaushev
▴ 10
1
vote
3
replies
620
views
warning when creating salmon index from GENCODE transcriptome
salmon
RNA-Seq
updated 13 months ago by
Rob
4.6k • written 13 months ago by
vaushev
▴ 10
3
votes
4
replies
1.2k
views
Library type warning in Salmon
Salmon
RNAseq
library-type
updated 13 months ago by
Biostar
20 • written 3.0 years ago by
grant.hovhannisyan
★ 2.1k
0
votes
0
replies
358
views
Issue with Salmon and Deseq2 with paired-end and single-end reads libraries
salmon
deseq2
rnaseq
tximport
14 months ago by
Andrés Ribone
• 0
145 results • Page
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