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Limit : this week
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116 results • Page
1 of 3
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
15
views
Alignment with new reference
alignment
50 minutes ago by
marco.barr
▴ 30
0
votes
1
reply
18
views
Mapping ortholog human and mouse transcript
biomart
updated just now by
manaswwm
▴ 490 • written 2 hours ago by
1769mkc
★ 1.2k
0
votes
0
replies
20
views
Bowtie2 alignment rate
galaxy
alignment
Bowtie
rate
3 hours ago by
pavithraashokkumar818
• 0
0
votes
0
replies
19
views
Variant calling of GBS data for polyploid plant
GBS
variants
polyploid
plant
4 hours ago by
analyst
▴ 10
0
votes
0
replies
26
views
Convert to ENTREZGENE
maize
ENTREZGENE
6 hours ago by
sansan_96
▴ 50
1
vote
0
replies
34
views
Synthetic lethality and cancer database
interaction
lethal
synthetic
8 hours ago by
Shicheng Guo
★ 9.4k
0
votes
0
replies
38
views
Tissue specific mRNA expression dataset in human and mouse
tissue
specificity
9 hours ago by
Shicheng Guo
★ 9.4k
0
votes
1
reply
89
views
vcf file: number of samples does not match number of columns
vcf
bcftools
updated 11 hours ago by
Pierre Lindenbaum
160k • written 11 hours ago by
ekirsch
• 0
0
votes
4
replies
200
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
10 hours ago by
BRENO
• 0
0
votes
2
replies
119
views
Error running local blastn in R using system2
blastn
NCBI
R
updated 10 hours ago by
Mensur Dlakic
★ 26k • written 13 hours ago by
Harrison
• 0
0
votes
1
reply
73
views
Looking for RPIP Illumina kit probe sequences
Sequences
Illumina
updated 15 hours ago by
GenoMax
140k • written 16 hours ago by
David Tachiquín
• 0
0
votes
9
replies
289
views
Low number of both surviving reads after trimming
trimmomatic
trimming
10 hours ago by
Jay
• 0
1
vote
2
replies
97
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
30 minutes ago by
Mohamed Abderrahmane
▴ 10
3
votes
2
replies
109
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
17 hours ago by
DYLAN NICO
• 0
0
votes
0
replies
65
views
Contradictions in GSEA results
GSEA
Enrichment-analysis
PEA
updated 18 hours ago by
Ram
43k • written 18 hours ago by
Tolga
▴ 20
0
votes
0
replies
60
views
Illumina Dna Prep kit for sequencing phage linear genomes
tagmentation
transposons
phagetermini
sequencing
18 hours ago by
alenew.am
• 0
0
votes
3
replies
351
views
FindAllMarkers not working (Error (data layers are not joined. Please run JoinLayersWarning: When testing 1 versus all)
FindAllMarkers
seurat
re-clustering
18 hours ago by
Nitin
• 0
0
votes
1
reply
96
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
scRNA-seq
updated 18 hours ago by
Ram
43k • written 19 hours ago by
chiditatawmbi
• 0
0
votes
1
reply
118
views
Normalization strategies for comparing mapped reads across samples in RNA-seq
normalization
rnaseq
updated 18 hours ago by
Ram
43k • written 19 hours ago by
Picasa
▴ 640
0
votes
0
replies
78
views
How to change alternate conformation occupancy ?
Bio.PDB.Atom
Bio.PDB
biopython
updated 18 hours ago by
Ram
43k • written 20 hours ago by
udakshi
• 0
0
votes
0
replies
97
views
Training
chip-seq
ScATAC-seq
20 hours ago by
Manhezz
• 0
1
vote
2
replies
126
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 17 hours ago by
Ram
43k • written 21 hours ago by
gdfsnkfns
• 0
1
vote
11
replies
308
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
updated 16 hours ago by
GenoMax
140k • written 22 hours ago by
Lila M
★ 1.2k
2
votes
2
replies
127
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
updated 17 hours ago by
dariober
14k • written 22 hours ago by
Pumla
• 0
0
votes
1
reply
97
views
Merging featureCounts output for different species
featureCounts
RNA-seq
updated 14 hours ago by
Ram
43k • written 23 hours ago by
Christian
• 0
0
votes
0
replies
76
views
Combine rename and rmdup in SeqKit to remove duplicate sequences and append N in header? Sort by occurence?
seqkit
fasta
23 hours ago by
Broccoli
• 0
0
votes
0
replies
72
views
Is there a good tool/reference for PBP and porin analysis
PBP
porin
23 hours ago by
blur
▴ 280
0
votes
0
replies
85
views
meta-analysis on RNA seq AND microarray results
microarray
RNA
1 day ago by
liuyibin2005
• 0
0
votes
0
replies
71
views
SPOTlight deconvolution logFC, logFC cohen or mean.AUC
spatial-transcriptomics
SPOTlight
logFC
deconvolution
updated 18 hours ago by
Ram
43k • written 1 day ago by
M'zelle
• 0
0
votes
0
replies
93
views
In scRNA, How should I set QC standards?
scRNA
QC
1 day ago by
mnx0723
• 0
0
votes
0
replies
89
views
How to check if a few pathways have relationship?
MSigdb
REACTOME
KEGG
1 day ago by
Chris
▴ 260
2
votes
10
replies
728
views
Only one read per run - Trying to use CellRangerv7
Fastq
CellRanger
updated 18 hours ago by
Ram
43k • written 5 weeks ago by
Sky
▴ 10
0
votes
0
replies
100
views
doing some ontology enrichment analysis
GO
1 day ago by
aleksk779
• 0
0
votes
2
replies
164
views
novel and know mir156 and mir172
a
updated 1 day ago by
gayachit
▴ 200 • written 1 day ago by
Fadmo
• 0
2
votes
8
replies
263
views
Piping samtools to R
R
NGS
bash
samtools
1 day ago by
joe
▴ 470
0
votes
8
replies
419
views
STAR aligner options
STAR
23 hours ago by
theophile
• 0
0
votes
2
replies
165
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
1 day ago by
Ankit
▴ 500
0
votes
1
reply
108
views
Wanting to make a Venn diagram of ATACseq peak files, unsure of where to start
ATAC-seq
updated 1 day ago by
Yogi
▴ 70 • written 1 day ago by
Ronin
• 0
0
votes
0
replies
81
views
Association Module to traits
module-trait-relationships
WGCNA
GENIE3
DOMINO
updated 1 day ago by
Ram
43k • written 1 day ago by
r.shiasi3897
▴ 10
0
votes
0
replies
85
views
Number of pathway result from GSVA
GSVA
1 day ago by
Chris
▴ 260
0
votes
1
reply
125
views
How can I remove duplicate SNP?
plink
updated 1 day ago by
iraun
6.2k • written 1 day ago by
Zhennan
• 0
0
votes
1
reply
133
views
SNP VCF files from hybrid populations and parental populations generated by GBS in public databases
contaminations
verification
parental
check
updated 1 day ago by
Ram
43k • written 1 day ago by
Hajar
• 0
0
votes
0
replies
78
views
Creating a custom ontology for peptides
ontology
peptide
1 day ago by
Mathew
• 0
0
votes
0
replies
79
views
GSEA number dimension of expression dataset
GSEA
1 day ago by
edoardofilippi1998
• 0
0
votes
0
replies
85
views
single cell data integration approach
comparison
integration
pairwise
singlecell
1 day ago by
Jay
• 0
0
votes
3
replies
217
views
High number of detected genes per cell after doublet removal - scRNAseq data
scRNAseq
duoblet
1 day ago by
sarahmanderni
▴ 100
0
votes
2
replies
155
views
Error with goodSamplesGenes()
R
WGCNA
1 day ago by
bioinfo_enthusiast
• 0
0
votes
0
replies
92
views
Variant Enrichment Analysis
Analysis
Enrichment
VEP
Variant
1 day ago by
Mojtaba
• 0
0
votes
7
replies
324
views
Salmon Quantification in Alignment based-mode
Salmon
RNA-seq
TPM
updated 1 day ago by
GenoMax
140k • written 1 day ago by
Patadu94
• 0
0
votes
1
reply
146
views
dbsnp flanks information
dbsnp
updated 2 days ago by
Pierre Lindenbaum
160k • written 2 days ago by
sskimvd
• 0
116 results • Page
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Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Recent Replies
Comment: Mapping ortholog human and mouse transcript
by
manaswwm
▴ 490
I usually perform biomaRt queries with their `getBM()` function where I list the input using `filter` and `values` option and my request in…
Comment: DESeq2 and normalization
by
JH
• 0
Thank you for your response. I have often seen commands like dds <- estimateSizeFactors(dds) normalized_counts <- counts(dds, normalized=T…
Comment: Number of CPUs to use by DRAP for transcriptomic assmbly
by
Mohamed Abderrahmane
▴ 10
It's the case that there's no indication of multi-threading in the documentation. However, it made me wonder why the developers would restr…
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
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