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35 results • Page
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Showing top results for tag:
Kallisto
•
reset
3
votes
8
replies
876
views
Kallisto: to scaledTPM or not to scaledTPM
tximport
kallisto
EdgeR
RNAseq
updated 16 days ago by
Gordon Smyth
★ 7.4k • written 20 days ago by
IM
• 0
0
votes
3
replies
422
views
Script for Rstudio
Rstudio
Transcript
kallisto
analysis
updated 26 days ago by
dsull
★ 6.8k • written 4 weeks ago by
Pumla
• 0
0
votes
1
reply
272
views
unmapped reads Kallisto bulk RNA-seq
kallisto
RNA-seq
unmapped-reads
updated 7 weeks ago by
Ram
44k • written 7 weeks ago by
Irene
• 0
4
votes
9
replies
736
views
Kallisto - Effect of Kmer size on quantification?
Kallisto
single-overhang
Kmer
RNA-seq
length
9 weeks ago by
jayeshkumarsundaram
• 0
2
votes
2
replies
280
views
kb count -x parameter - what are the three parts?
kb_python
umi
cell-barcodes
kallisto
updated 10 weeks ago by
Assa Yeroslaviz
★ 1.9k • written 10 weeks ago by
gogeni5529
▴ 50
2
votes
1
reply
293
views
I am getting an error with Kallisto Bustools wrapper (kb) command to create an index
kb
kallisto
bustools
updated 11 weeks ago by
dsull
★ 6.8k • written 11 weeks ago by
biotrekker
▴ 100
2
votes
2
replies
425
views
Is the 10X multiome chemistry most similar similar to 10XV1, 10XV2, or 10XV3?
snRNAseq
kallisto
10X
11 weeks ago by
biotrekker
▴ 100
4
votes
3
replies
454
views
gene ids do not have corresponding valid gene names kallisto bus tools
mapping
kallisto
bustools
updated 12 weeks ago by
dsull
★ 6.8k • written 12 weeks ago by
naili mortadha
• 0
2
votes
4
replies
442
views
indexing the drosophila genome for kallisto
index
kallisto
12 weeks ago by
gogeni5529
▴ 50
4
votes
2
replies
573
views
Understanding Differing results between STAR and kallisto
quantification
STAR
kallisto
RNA-Seq
updated 3 months ago by
rfran010
★ 1.3k • written 3 months ago by
Assa Yeroslaviz
★ 1.9k
1
vote
2
replies
317
views
scaling for kallisto estimate counts
Differential-gene-expression
RNAlysis
Kallisto
3 months ago by
Meghan.T
• 0
0
votes
6
replies
566
views
Why am I getting such a big difference in alignment rates in kallisto?
kallisto
ensembl
3 months ago by
bioinfo
▴ 150
2
votes
2
replies
362
views
getting RNA-seq raw counts from Kallisto
counts
raw
RNA-seq
Kallisto
3 months ago by
Meghan.T
• 0
1
vote
3
replies
441
views
Can I go from kallisto results to SEURAT directly
cell
bustoolls
kallisto
single
updated 3 months ago by
dsull
★ 6.8k • written 3 months ago by
biotrekker
▴ 100
2
votes
2
replies
735
views
Salmon vs Kallisto vs RSEM
RSEM
quantification
kallisto
Salmon
4 months ago by
Mohamed Abderrahmane
▴ 20
2
votes
3
replies
493
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
15 hours ago by
bioinfo
▴ 150
1
vote
5
replies
944
views
How should I make kallisto indexes?
kallisto
updated 5 months ago by
dsull
★ 6.8k • written 5 months ago by
bioinfo
▴ 150
3
votes
2
replies
555
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 5 months ago by
dsull
★ 6.8k • written 5 months ago by
Aaliya
▴ 10
1
vote
2
replies
429
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
5 months ago by
bioinfo
▴ 150
2
votes
6
replies
1.1k
views
Kallisto returns 'illegal instruction' when running commands
kallisto
rna-seq
updated 6 months ago by
GenoMax
145k • written 6 months ago by
Eleanor
• 0
0
votes
1
reply
364
views
Using tophat2 output for kallisto
bam
tophat2
kallisto
updated 7 months ago by
dsull
★ 6.8k • written 7 months ago by
Wintermute
• 0
3
votes
7
replies
851
views
How does kallisto handle multi mapped reads?
kallisto
updated 7 months ago by
dsull
★ 6.8k • written 7 months ago by
bioinfo
▴ 150
1
vote
2
replies
558
views
How to do DESeq2 on Kallisto Data
Unfolded
Kallisto
DESeq2
Reponse
Protein
updated 7 months ago by
dsull
★ 6.8k • written 7 months ago by
Aaliya
• 0
0
votes
4
replies
566
views
isoformSwithAnalyzeR importRdata error
tximport
h5
isoformSwitchAnalyzeR
kallisto
updated 8 months ago by
i.sudbery
20k • written 8 months ago by
bsmith030465
▴ 240
1
vote
3
replies
731
views
Kallisto-Bustools Output prpblems
Bustools
Kallisto
updated 9 months ago by
dsull
★ 6.8k • written 9 months ago by
myoui3122010
▴ 20
3
votes
3
replies
821
views
Kallisto-bustools output to Seurat Object
Bustools
Kallisto
Seurat
updated 9 months ago by
GenoMax
145k • written 9 months ago by
myoui3122010
▴ 20
2
votes
5
replies
1.1k
views
kallisto index build difference according to version
index
version
kallisto
updated 10 months ago by
dsull
★ 6.8k • written 10 months ago by
estilo
• 0
2
votes
6
replies
1.0k
views
Quality filtering prior to pseudoalignment
fastp
rna-seq
pseudoalignment
kallisto
updated 10 months ago by
Brian Bushnell
20k • written 10 months ago by
Roberto
▴ 20
3
votes
4
replies
896
views
Why am I getting different results with kallisto?
kallisto
10 months ago by
bioinfo
▴ 150
3
votes
4
replies
1.2k
views
Kallisto abundance.tsv
Kallisto
updated 11 months ago by
Ram
44k • written 11 months ago by
sansan96
▴ 130
1
vote
4
replies
915
views
How to assign gene names after kallisto when I add GFP?
tximport
RNA-seq
kallisto
11 months ago by
bioinfo
▴ 150
6
votes
3
replies
792
views
kallisto normalized TPM values without bootstraps
tpm
cibersort
sleuth
kallisto
RNA-seq
updated 28 days ago by
binbinZhao
• 0 • written 12 months ago by
butterman16
▴ 30
3
votes
0
replies
1.4k
views
Tutorial:
Analysis of Smart-Seq3 data with kallisto-bustools
single-cell
kallisto
transcriptomics
smart-seq3
pipeline
updated 10 months ago by
Ali
• 0 • written 20 months ago by
firestar
★ 1.6k
5
votes
4
replies
2.4k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts
DESEQ2
differential-gene-expression
kallisto
updated 5 months ago by
Ram
44k • written 3.2 years ago by
mrj
▴ 180
0
votes
1
reply
2.1k
views
Is it appropriate to apply RUVseq on output from kallisto?
RNA-Seq
batch-correction
kallisto
updated 5 months ago by
Ram
44k • written 5.7 years ago by
unawaz
▴ 60
35 results • Page
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Comment: When to use integration with scRNASeq
Answer: Using GEOquery
Answer: Using GEOquery
Comment: Using GEOquery
Comment: Using GEOquery
Comment: Using GEOquery
Comment: how to get visium HD dataset with its information
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Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Michael
55k
Ok, that's quite common but can cause a lot of fuzz (if you notice it, even more if it goes unnoticed). Try to check the md5 sums generated…
Comment: Visualizing Upregulated and Downregulated Genes in GO and KEGG Pathway Analyses
by
Nat.Nataren
▴ 90
Depends on the output your are getting, say its something like below, saved in a dataframe `df` that countains your `FoldEnrichment` values…
Comment: how to get visium HD dataset with its information
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Nat.Nataren
▴ 90
Might also be worth looking at the CELLxGENE database and selecting Visium datasets. The corresponding publication may provide the addition…
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heureuse
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Not for that but to know the % of CNV inherited in order to know the sensitivity of the caller
Comment: Mendelian precison
by
heureuse
• 0
This is really helpful and beyond what I've expected. Thank you
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by
Jaber
• 0
Thank you, I already extracted manually, as I am using WSL, and directories are correct, and I still get the error saying "Segmentation fa…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
Thx. I found out that I used the wrong reference genome. I have a set of data from mice and a set from humans. I processed the human data u…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
Thx. It turns out that the file was damaged during transmission.
Comment: how to get visium HD dataset with its information
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145k
Depending on how much of that information is personally identifiable you may not be able to get the metadata unless you get approval from d…
Comment: HTseq count issue, not aligning to features
by
GenoMax
145k
Have you examined the alignments with IGV or a similar genome browser? Are the reads aligning in correct place (e.g. under exons). Also try…
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★ 28k
It is very difficult to follow al the lines as your script content are not properly formatted. It appears that in one command you are do…
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84k
Have you even read my answer? I gave a full explanation on what the problem is and what the solutions can be. What is unclear?
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I also come up with this problem. No body still answer this question.
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You can use the `bio` with the `align` tool. Install with `pip install bio` then bio align query.fa target.fa You can put all the tar…
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Since they explicitly have a pbsim config file, the comment you found is probably just a leftover from another config file that was copied …
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