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50 results • Page
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Showing top results for tag:
umi
•
reset
0
votes
0
replies
156
views
Fusion analysis with UMI deduplication
UMI
Fusion
deduplication
Star
14 days ago by
Xira_D
• 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
5
votes
4
replies
395
views
Multiple same UMI's mapped to the same cell with different sequence
10x
UMI
BAM
scRNAseq
Barcode
11 weeks ago by
zbidav
▴ 30
2
votes
2
replies
351
views
Infer UMI from fastq files
bcl2fastq
transcriptome
RNA-seq
UMI
3 months ago by
Ar
★ 1.1k
6
votes
5
replies
581
views
Extracting UMIs from NEXTFLEX Small RNA-Seq reads using UMI_tools
smallRNAseq
UMI
NEXTflex
UMI_tools
miRNA
updated 3 months ago by
i.sudbery
20k • written 3 months ago by
MH85
▴ 20
0
votes
4
replies
374
views
How to Split FASTQ File by UMI Indices into Multiple Files
SeqKit
UMI
split
fastq
updated 4 months ago by
GenoMax
145k • written 4 months ago by
LDT
▴ 340
0
votes
1
reply
291
views
Can I count UMI-barcode combination without mapping?
HyDrop
protein
UMI
UMI-Tools
updated 4 months ago by
GenoMax
145k • written 4 months ago by
Assa Yeroslaviz
★ 1.9k
3
votes
2
replies
410
views
Is there any minimum number of counts in scRNAseq to consider that a gene is expressed?
scRNAseq
single-cell
seurat
scanpy
UMI
3 months ago by
ev97
▴ 30
5
votes
12
replies
1.0k
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 4 months ago by
i.sudbery
20k • written 4 months ago by
Assa Yeroslaviz
★ 1.9k
0
votes
2
replies
1.0k
views
AGeNT LocatIt
AGeNT
LocatIt
WES
UMI
duplicates
updated 5 months ago by
barslmn
★ 2.3k • written 3.2 years ago by
jhy
▴ 10
2
votes
5
replies
767
views
Marking duplicates using UMIs
Deduplication
UMI
updated 5 months ago by
i.sudbery
20k • written 5 months ago by
Lipika
• 0
0
votes
1
reply
333
views
Extract Umi sequence to readname
Sequence
FgBio
UMI
updated 6 months ago by
GenoMax
145k • written 6 months ago by
Smilesky
• 0
1
vote
5
replies
721
views
UMI_extract for paired end reads of micro_RNA
UMI-tools
UMI
miRNA
updated 6 months ago by
ATpoint
84k • written 6 months ago by
otieno43
▴ 30
0
votes
6
replies
836
views
Multiple unique reads sharing same UMI barcode
umi
ngs
updated 7 months ago by
i.sudbery
20k • written 7 months ago by
ww22runner
▴ 60
0
votes
1
reply
538
views
Calling variants with UMI-collapsed duplex consensus reads
Mutect2
CallDuplexConsensusReads
fgbio
UMI
updated 7 months ago by
Ram
44k • written 7 months ago by
blid11
• 0
2
votes
2
replies
605
views
UMI workflow resulting in bams with empty reads
umi
7 months ago by
ww22runner
▴ 60
0
votes
2
replies
376
views
Is it possible to identify the strand of an RNA using UMI?
high-throughput
UMI
sRNA
Qiagen
RNA-seq
updated 8 months ago by
i.sudbery
20k • written 8 months ago by
Carolina
• 0
0
votes
3
replies
576
views
Mapping paired end
dna-seq
mapping
umi
umitools
ngs
7 months ago by
Sarah
• 0
0
votes
7
replies
1.0k
views
UMI-tools no tsv files at deduplication
deduplication
NGS
UMI
DNA-seq
UMI-tools
updated 8 months ago by
Ram
44k • written 8 months ago by
Sarah
• 0
1
vote
1
reply
646
views
DNA sequencing workflow involving UMIs
dna
umi
sequencing
updated 8 months ago by
Matthias Zepper
4.9k • written 8 months ago by
ww22runner
▴ 60
0
votes
3
replies
944
views
Deduplication
UMI
UMI_TOOLS
removal
Deduplication
PCR-duplicate
updated 11 months ago by
Brian Bushnell
20k • written 14 months ago by
tanmoymukherjee07
• 0
0
votes
0
replies
335
views
Is it valid to use UMI-based analysis pipelines for aptamer-based proteomics
UMI
aptamer
RNA-seq
proteomics
16 months ago by
Ali
• 0
0
votes
0
replies
544
views
Analyse UMI using picard's ExtractIlluminaBarcodes & IlluminaBasecallsToSam with 2 or 4 lanes
picard
umi
17 months ago by
User000
▴ 710
0
votes
3
replies
852
views
UMI in seqc2 dataset Burning Rock data
sequencing
UMI
updated 17 months ago by
LChart
4.3k • written 17 months ago by
PeterWu
▴ 20
1
vote
2
replies
617
views
In Silico Fast.gz files for UMI data? (Unique Molecular Identifiers)
fastq
in-silico
umi
17 months ago by
Michael
▴ 10
2
votes
3
replies
939
views
Why can’t we have full-length transcripts with droplet-based technologies ?
single-cell
UMI
smart-seq3
18 months ago by
sagane.joye
• 0
1
vote
2
replies
1.3k
views
How can I use bcftools mpileup or an alternative to find ALL variants without any probabilistic inference?
Fgbio
UMI
variant-calling
18 months ago by
chaco001
▴ 40
2
votes
1
reply
845
views
Adding MBC/UMI RX tag to read name
umi
18 months ago by
Christian
▴ 40
0
votes
2
replies
866
views
Cellranger count creating an empty matrix.mtx after adding 'N' and '#' to R1 UMI and quality respectively to account for 9bp UMI.
scRNA-seq
UMI
cellranger
aligning
19 months ago by
JHorder
• 0
16
votes
7
replies
2.5k
views
BULK mRNA-seq with UMIs. Do I need to normalize by gene length?
mRNA
UMI
normalization
illumina
DESeq2
updated 20 months ago by
Matthias Zepper
4.9k • written 20 months ago by
txema.heredia
▴ 180
3
votes
5
replies
1.7k
views
UMI-tools deduplication of reads with UMI at the start of the line
UMI
UMI-tools
updated 15 months ago by
Ram
44k • written 20 months ago by
Uri
• 0
8
votes
10
replies
6.3k
views
Extract UMIs using UMI-tools
UMI
UMI-tools
updated 22 months ago by
Matthias Zepper
4.9k • written 2.4 years ago by
I.Kim
▴ 40
2
votes
3
replies
781
views
Extract list of mapped UMIs in cell ranger output
UMI
cellranger
RNAseq
bam
10X
22 months ago by
miguellarrazlopezdenovales
▴ 20
5
votes
5
replies
2.4k
views
UMI deduplication and output
UMI
deduplication
updated 14 months ago by
i.sudbery
20k • written 23 months ago by
Elise
• 0
4
votes
4
replies
932
views
how to handle the UMI sequence of Immune Repertoire sequencing .fastq data
fastp
Immune
Repertoire
IR-SEQ
pandaseq
sequencing
UMI
2.0 years ago by
Yuki _ISHIKAWA
▴ 20
0
votes
2
replies
775
views
10x scRNAseq samples with similar reads/cell but vastly differing UMI/cell
10x
scRNAseq
UMI
QC
2.1 years ago by
matt.a.bennett25890
▴ 30
3
votes
2
replies
800
views
CNVKit on targeted amplicons with UMIs
CNVKit
UMI
updated 2.1 years ago by
Eric T.
★ 2.8k • written 2.2 years ago by
Sophie
▴ 10
0
votes
0
replies
423
views
How does bcl-convert handle UMIs in the 3' end of the insert
umi
illumina
bcl-convert
2.2 years ago by
ingerslev
• 0
0
votes
2
replies
998
views
Detecting duplicated UMI in BAM file
UMI
BAM
2.3 years ago by
tien
▴ 40
4
votes
4
replies
988
views
Renaming reads
fastq
rename
sed
UMI
2.3 years ago by
vvs.hazia
▴ 10
0
votes
4
replies
899
views
Decipher 3' 10X paired-end reads
umi
barcode
2.4 years ago by
tvibhaps
▴ 10
1
vote
1
reply
496
views
Libraries with different size in the same MiniSeq cartridge
Illumina
MiniSeq
UMI
updated 18 months ago by
Ram
44k • written 2.5 years ago by
MH85
▴ 20
2
votes
3
replies
892
views
Deduplication of umi from my celseqdata
SinglecellRNA
umi
cellseq
cellseq2
barcode
2.6 years ago by
Parichitran
• 0
0
votes
1
reply
500
views
How to call snps on sequencing data that contains UMIs
Galaxy
UMI
DNA-seq
updated 2.6 years ago by
Istvan Albert
101k • written 2.6 years ago by
mathilde.thierry
▴ 10
0
votes
0
replies
445
views
fgbio read structure
fgbio
UMI
ExtractUmisFromBam
2.8 years ago by
MH85
▴ 20
2
votes
2
replies
865
views
Simulating illumina sequences with UMI data
sequencing
genotyping
umi
simulating
illumina
2.8 years ago by
Stefan
▴ 10
2
votes
4
replies
2.1k
views
UMI extraction from 10X visium spatial transcriptome data
umi_tools
UMI
spatial-transcriptome
updated 15 months ago by
Ram
44k • written 2.8 years ago by
Omics data mining
▴ 260
0
votes
0
replies
622
views
Extracting internal reads from SmartSeq3 data using zUMIs
internal
UMI
zUMIs
reads
SmartSeq3
2.8 years ago by
pm2012
▴ 140
0
votes
1
reply
1.6k
views
bcl-convert and UMI's
bcl-convert
UMI
updated 2.8 years ago by
GenoMax
145k • written 2.8 years ago by
matthias.desmet
▴ 30
0
votes
0
replies
533
views
How to Analyze Read Counts datasets and UMI-Counts datasets in scRNA-seq
reads
scrna-seq
UMI
2.9 years ago by
ksaunders73
▴ 10
50 results • Page
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Recent Votes
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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164k
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Recent Replies
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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by
Istvan Albert
101k
Since they explicitly have a pbsim config file, the comment you found is probably just a leftover from another config file that was copied …
Comment: RNA-Seq mutation calling without germline data
by
marionette.kent
• 0
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…
Comment: Pedigree information
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bk11
★ 3.0k
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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