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33 results • Page
1 of 1
Sort: Views
Rank
Views
Votes
Replies
2
votes
10
replies
700
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 3 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
1
vote
12
replies
512
views
Nanopore data filtering using fastp
fastp
nanopore
2 hours ago by
emilydolivo97
• 0
0
votes
9
replies
453
views
Nextflow ERROR : Timeout waiting for connection from pool
nextflow
updated 6 hours ago by
GenoMax
140k • written 6 days ago by
dzisis1986
▴ 70
0
votes
8
replies
412
views
STAR aligner options
STAR
8 hours ago by
theophile
• 0
0
votes
7
replies
312
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 19 hours ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
5
replies
299
views
Parsing fasta file by coordinates
linux
fasta
updated 1 hour ago by
GenoMax
140k • written 2 days ago by
sorrymouse
▴ 120
2
votes
8
replies
246
views
Piping samtools to R
R
NGS
bash
samtools
22 hours ago by
joe
▴ 470
0
votes
4
replies
242
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq
STAR
IGV
6 hours ago by
rohitsatyam102
▴ 840
1
vote
11
replies
241
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 54 minutes ago by
GenoMax
140k • written 6 hours ago by
Lila M
★ 1.2k
0
votes
3
replies
223
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
2 hours ago by
Nitin
• 0
0
votes
2
replies
159
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
20 hours ago by
Ankit
▴ 500
0
votes
2
replies
150
views
novel and know mir156 and mir172
a
updated 18 hours ago by
gayachit
▴ 200 • written 21 hours ago by
Fadmo
• 0
2
votes
2
replies
85
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 2 hours ago by
dariober
14k • written 7 hours ago by
Pumla
• 0
0
votes
1
reply
83
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 3 hours ago by
Ram
43k • written 4 hours ago by
Picasa
▴ 640
0
votes
0
replies
80
views
doing some ontology enrichment analysis
GO
18 hours ago by
aleksk779
• 0
1
vote
2
replies
79
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 1 hour ago by
Ram
43k • written 6 hours ago by
gdfsnkfns
• 0
0
votes
1
reply
72
views
Merging featureCounts output for different species
featureCount
RNAseq
updated 8 hours ago by
andrebolerbarros
• 0 • written 8 hours ago by
Christian
• 0
0
votes
0
replies
68
views
Training
chip-seq
ScATAC-seq
5 hours ago by
Manhezz
• 0
0
votes
0
replies
66
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
15 hours ago by
Chris
▴ 260
0
votes
0
replies
65
views
In scRNA, How should I set QC standards?
scRNA
QC
12 hours ago by
mnx0723
• 0
0
votes
1
reply
58
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 3 hours ago by
Ram
43k • written 3 hours ago by
chiditatawmbi
• 0
2
votes
2
replies
56
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
2 hours ago by
DYLAN NICO
• 0
0
votes
0
replies
56
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
9 hours ago by
liuyibin2005
• 0
0
votes
0
replies
51
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 2 hours ago by
Ram
43k • written 5 hours ago by
udakshi
• 0
0
votes
0
replies
49
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
8 hours ago by
Broccoli
• 0
0
votes
0
replies
49
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
8 hours ago by
blur
▴ 280
0
votes
0
replies
46
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 3 hours ago by
Ram
43k • written 9 hours ago by
M'zelle
• 0
0
votes
1
reply
37
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
updated 44 minutes ago by
GenoMax
140k • written 2 hours ago by
Mohamed Abderrahmane
▴ 10
0
votes
0
replies
34
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 3 hours ago by
Ram
43k • written 3 hours ago by
Tolga
▴ 20
0
votes
2
replies
33
views
Low number of both surviving reads after trimming
trimmomatic
trimming
updated 51 minutes ago by
GenoMax
140k • written 1 hour ago by
Jay
• 0
0
votes
0
replies
30
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
3 hours ago by
alenew.am
• 0
0
votes
1
reply
17
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 40 minutes ago by
GenoMax
140k • written 1 hour ago by
David Tachiquín
• 0
0
votes
0
replies
10
views
Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
scRNA
RNAseq
18 minutes ago by
sithlordashley
• 0
33 results • Page
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Recent Votes
Answer: Demonstrating lack of difference between two peaksets
Comment: Input arguments for AddOrReplaceReadGroups (Picard) from fastq
Answer: Input arguments for AddOrReplaceReadGroups (Picard) from fastq
Input arguments for AddOrReplaceReadGroups (Picard) from fastq
Comment: Variant calling of GBS data
Comment: Flow Cytometry Data Analysis by Seurat
C: Which human reference genome should I use?
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Recent Awards •
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Commentator
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GenoMax
140k
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Ann
★ 2.4k
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to
Devon Ryan
104k
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amitpande74
▴ 20
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Pierre Lindenbaum
160k
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beacamara
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blur
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Recent Replies
Answer: Annotation of Complex genomes using NCBI Genome Workbench
by
Lissa Cruz Saavedra
• 0
Hi Recently, I used https://www.gensas.org/ to make the annotation. It was pretty practical and in my opinion easy. You just need to up…
Comment: Hybrid assembly Pacbio- Nanopore
by
Lissa Cruz Saavedra
• 0
Hi Thanks for your answer. I think I have very good coverage. My genome size is 48M. I also have data from poreC and illumina, the last on…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Anyone please suggest which variant caller can be the best choice for variant calling of GBS data for polyploid plant.
Comment: Variant calling of GBS data
by
analyst
▴ 10
Does GATK Haplotypecaller take care of ploidy because few plants are polyploid?
Comment: Looking for RPIP Illumina kit probe sequences
by
GenoMax
140k
More than likely they will only be available in the accompanying analysis app (Explify RPIP) in BaseSpace. Check with Illumina tech support…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Mensur Dlakic
★ 26k
Pretty sure I have done it, but can't remember the details. You know that thing about blocking out traumatic events ...
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
GenoMax
140k
> I have just noticed in the documentation that there is no argument to specify the number of CPUs to use for calculations. If the program…
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
Do you have a plot of adapter contamination for this data from FastQC? If you have a lot of adapter dimers, short inserts i.e. bad quality…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Looks like those appear to be "polycomb associated non-coding RNA". You probably know what they are. https://www.ncbi.nlm.nih.gov/nuccore/…
Comment: Parsing fasta file by coordinates
by
GenoMax
140k
> sequences that are from the same region from those that aren't. could refer to sequence composition and that is the reason we were sugge…
Comment: Low number of both surviving reads after trimming
by
Ram
43k
Please edit your post and add the code parts again, this time use the `101010` code button and NOT the double quote button. The latter is u…
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Pierre Lindenbaum
160k
... reminds me [https://twitter.com/yokofakun/status/1267877851795259397][1] ( my twitter account is now private) ![ops][2] [1]: https…
Comment: Flow Cytometry Data Analysis by Seurat
by
Ram
43k
Why did you delete this post, https://www.biostars.org/u/142036/ ?
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
dariober
14k
Perhaps more concerning is why you have features (genes?) with small pvalue but fold-change very close to zero. It's also unusual that ther…
Comment: Gene reads all zero for each sample
by
DYLAN NICO
• 0
Thank you for the suggestions. Unfortunately I cannot add any details for lack of information. But I will try using a different alignment a…
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