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Showing top results for tag: Kallisto • reset
118
votes
26
replies
37k
views
22 follow
Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
DESeq Kallisto RNASeq Salmon DESeq2
updated 19 months ago by ▴ 230 • written 9.4 years ago by ▴ 610
48
votes
24
replies
8.6k
views
14 follow
Tool: Hera: A new tool for RNA-Seq analysis
kallisto RNA-Seq STAR gene-fusion
updated 15 months ago by 44k • written 7.2 years ago by ▴ 580
58
votes
19
replies
21k
views
11 follow
Current state-of-the-art for RNA-Seq gene / transcript expression quantification OR just the tools of preference
kallisto salmon bitseq RNA-Seq cufflinks
updated 2.0 years ago by 44k • written 9.1 years ago by ★ 1.3k
8
votes
17
replies
3.6k
views
8 follow
What does the fragment length (-l) argument in Kallisto actually do?
Kallisto Pseudoalignment RNA-seq
updated 20 months ago by ★ 6.8k • written 23 months ago by ▴ 40
54
votes
16
replies
5.9k
views
13 follow
Forum: The new era of bioinformatics: simple and fast tools, fewer and more informative data
kallisto computational-cost
updated 20 months ago by 44k • written 9.4 years ago by 101k
10
votes
15
replies
7.9k
views
6 follow
Kallisto pseudobam to IGV
RNA-Seq kallisto pseudobam IGV alignment
updated 6.6 years ago by ▴ 460 • written 7.2 years ago by ▴ 70
9
votes
15
replies
4.7k
views
Kallisto will not produce .bam files
kallisto RNA-Seq
updated 6.4 years ago by 88k • written 6.4 years ago by ▴ 640
8
votes
14
replies
2.8k
views
6 follow
kallisto pseudoalignment rate is lower than literature
pseudoalignment kallisto RNA-seq
3.2 years ago by johnsonqinz • 0
8
votes
13
replies
2.0k
views
Mapped reads not mapping to a real sequence?
bam sam samtools kallisto
19 months ago by txema.heredia ▴ 180
3
votes
13
replies
3.8k
views
How to choose parameters for kallisto single end mode?
kallisto RNA-seq
updated 16 months ago by 101k • written 23 months ago by ▴ 150
7
votes
11
replies
10k
views
7 follow
kallisto: strand-specific and fragment length calculation
RNA-Seq kallisto
updated 7.4 years ago by ▴ 130 • written 7.4 years ago by ▴ 380
1
vote
11
replies
3.5k
views
RNA-Seq without replicate using Kallisto
RNA-Seq Kallisto
8.0 years ago by weixiaokuan ▴ 140
3
votes
11
replies
2.6k
views
RNASeq reads from two bacterial species
RNA-Seq kallisto RSEM trinity co-culture
updated 7.6 years ago by 35k • written 7.6 years ago by • 0
7
votes
11
replies
3.4k
views
Tool: Graphical User Interface for creating an automated RNA-Sequencing Pipeline via Kallisto and DESeq2
DESeq2 kallisto RNA-Seq
updated 15 months ago by 44k • written 5.7 years ago by ▴ 60
5
votes
10
replies
3.5k
views
Predicted gene differentially expressed in Kallisto, not in FeatureCounts
Kallisto FeatureCounts
updated 6.5 years ago by 35k • written 6.5 years ago by 5.6k
2
votes
10
replies
3.2k
views
finding significance between transcripts in a RNA-Seq experiment
tximport deseq2 edger limma kallisto
8.1 years ago by Assa Yeroslaviz ★ 1.9k
7
votes
10
replies
1.9k
views
No expression found with Salmon and Kallisto
salmon rna-seq transcriptome kallisto
15 months ago by firefox91 • 0
0
votes
10
replies
2.6k
views
How to do DESeq2 for Kallisto
Kallisto rna-seq DESeq2
4.0 years ago by Kumar ▴ 170
11
votes
10
replies
2.1k
views
Issues with newer Kallisto versions (aka 0.46.1)
Kallisto
updated 2.3 years ago by ★ 6.8k • written 2.3 years ago by ★ 5.1k
5
votes
9
replies
3.3k
views
How to change my colnames(count.table) as exactly similar to my rownames(meta)?
RNA-Seq Kallisto DESeq2 R tximport
updated 5.2 years ago by 84k • written 5.2 years ago by ▴ 80
4
votes
9
replies
4.4k
views
kallisto + sleuth: no results
rna-seq R kallisto sleuth
updated 5.8 years ago by ▴ 20 • written 7.2 years ago by • 0
1
vote
9
replies
2.6k
views
kallisto bootstrap / condo installation problem
hfd5 kallisto condo
updated 17 months ago by ★ 6.8k • written 17 months ago by ▴ 10
11
votes
9
replies
9.2k
views
7 follow
Getting average fragment length for single end reads
RNA-Seq kallisto differential expresion
updated 6.4 years ago by ▴ 30 • written 7.4 years ago by ▴ 300
3
votes
9
replies
14k
views
Build a Kallisto transcriptome index
Kallisto RNA-Seq pseudo-alignment
updated 5.2 years ago by ▴ 700 • written 5.2 years ago by ▴ 80
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
18
votes
9
replies
5.0k
views
Is Sleuth a good package?
RNA-Seq R kallisto sleuth
5.9 years ago by scchess ▴ 640
3
votes
8
replies
3.9k
views
Blog: Salmon Kallisto HtSeq-count for gene level analysis - Anecdotal evidence
salmon kallisto RNA-Seq htseq-count
updated 21 months ago by 44k • written 9.3 years ago by 5.2k
2
votes
8
replies
4.1k
views
How to make a loop to run kallisto bus command for so many fastq.gz files at once?
bash kallisto bustools
updated 18 months ago by 44k • written 5.0 years ago by ▴ 80
3
votes
8
replies
2.3k
views
Kallisto mapping paired end
Kallisto mapping
updated 16 months ago by 44k • written 2.6 years ago by ▴ 20
1
vote
8
replies
5.2k
views
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : HDF5. File accessibilty. Unable to open file.
kallisto RNA-Seq biomaRt sleuth software error
updated 4.3 years ago by ▴ 20 • written 4.4 years ago by ▴ 10
16
votes
8
replies
15k
views
Confusion about FindMarkers(), FindVariableFeatures(), RunTSNE(), and RunUMAP() in seurat package
scRNA-seq kallisto Seurat bustools
updated 18 months ago by 44k • written 4.9 years ago by ▴ 80
2
votes
8
replies
5.3k
views
Minimal TPM threshold for qPCR measure of gene expression
qpcr RNA-Seq TPM kallisto tximport
6.9 years ago by tlorin ▴ 370
1
vote
8
replies
1.9k
views
Quantseq 3' seq alignment with kallisto
Quantseq kallisto
updated 23 months ago by 14k • written 23 months ago by • 0
3
votes
8
replies
876
views
Kallisto: to scaledTPM or not to scaledTPM
tximport kallisto EdgeR RNAseq
updated 16 days ago by ★ 7.4k • written 20 days ago by • 0
3
votes
8
replies
2.3k
views
Kallisto: Impact of chosen reference transcriptome on the resulting TPMs
RNA-Seq kallisto
updated 4.5 years ago by 20 • written 4.6 years ago by 6.2k
6
votes
8
replies
2.9k
views
bustools transcript to gene file
bustools kallisto scRNA nextflow ensembl
4.7 years ago by Barry Digby ★ 1.3k
9
votes
7
replies
2.7k
views
Building index with kallisto, keeps getting killed.
kallisto
updated 21 months ago by 55k • written 21 months ago by ▴ 40
0
votes
7
replies
1.7k
views
Kallisto M1 Macbook Pro
M1 rnaseq kallisto Mac
updated 2.6 years ago by 145k • written 2.6 years ago by • 0
5
votes
7
replies
2.4k
views
6 follow
Kallisto and Salmon give different results
transcript expression salmon hisat2 kallisto
updated 2.4 years ago by ★ 6.8k • written 2.4 years ago by ▴ 30
0
votes
7
replies
3.3k
views
Is Kallisto good for identifying non-coding RNA in a RNAseq data?
Allignment Kallisto RNA-Seq
updated 16 months ago by 44k • written 5.8 years ago by ▴ 10
2
votes
7
replies
4.2k
views
Visualizing alignment of kallisto .bam files to hg19 (and custom plasmids)
IGV kallisto RNA-Seq
updated 6.1 years ago by ▴ 130 • written 6.1 years ago by ▴ 640
3
votes
7
replies
2.6k
views
Discrepancy in number of pseudoaligned reads for read quantification with Kallisto
RNA-Seq kallisto pseudo-alignment
updated 4.5 years ago by 84k • written 4.5 years ago by • 0
10
votes
7
replies
5.4k
views
Alternative splicing analysis following kallisto?
RNA-Seq kallisto alternative splicing
updated 6.5 years ago by ★ 4.1k • written 6.5 years ago by ▴ 170
0
votes
7
replies
2.9k
views
How to perform gene annotation in kallisto?
Gene kallisto annotation
updated 13 months ago by • 0 • written 3.1 years ago by ▴ 100
1
vote
7
replies
2.7k
views
Kallisto | bustools workflow for fastq with R1 and R2 (forward and reverse)?
scRNA-seq Kallisto bustools
updated 18 months ago by 44k • written 5.0 years ago by ▴ 80
2
votes
7
replies
3.9k
views
Kallisto read count processed does not tally
Kallisto trim_galore
6.6 years ago by solyris83 ▴ 20
3
votes
7
replies
851
views
How does kallisto handle multi mapped reads?
kallisto
updated 7 months ago by ★ 6.8k • written 7 months ago by ▴ 150
0
votes
7
replies
1.4k
views
6 follow
How to create kallisto index that does not include ribosomal genes
enseml kallisto RNA-seq
updated 21 months ago by 44k • written 2.4 years ago by ▴ 150
1
vote
7
replies
1.9k
views
Accuracy of Methods for Gene Variant Detection and Quantification: Kallisto Pseudoalignment vs. STAR Alignment
kallisto STAR RNA-seq Transcript_variants
16 months ago by sohail.mbio • 0
14
votes
7
replies
7.4k
views
Sleuth: Combined lrt and wt tests, clustered heatmap
RNA-Seq Sleuth kallisto R heatmap
updated 6.9 years ago by ▴ 110 • written 7.8 years ago by ▴ 230
50 results • Page 1 of 1
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Comment: When to use integration with scRNASeq
Answer: Using GEOquery
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Comment: how to get visium HD dataset with its information
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Comment: how to get visium HD dataset with its information by Nat.Nataren ▴ 90
Might also be worth looking at the CELLxGENE database and selecting Visium datasets. The corresponding publication may provide the addition…
Comment: Mendelian precison by heureuse • 0
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
Answer: featureCounts segmentation fault 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 by GenoMax 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…
Answer: featureCounts segmentation fault by Mensur Dlakic ★ 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…
Comment: Using GEOquery by ATpoint 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?
Comment: Using GEOquery by Rohulla • 0
I also come up with this problem. No body still answer this question.
Answer: Performing Needleman-Wunsch Global Alignment for multiple mutant proteins agains by Istvan Albert 101k
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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Thanks @shred for sharing your pipeline. Can I ask if it runs each sample individually? Our HPC has limited space for each user so I have b…
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Since you have plink (bed/bim/fam) files, sex information is stored in the 5th column of the `.fam` file. If that information is missing an…
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