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173 results • Page
2 of 4
Sort: Votes
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Views
Votes
Replies
1
vote
2
replies
213
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 2 days ago by
Ram
43k • written 3 days ago by
Ravita
• 0
1
vote
2
replies
272
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
1 day ago by
Nafi
• 0
1
vote
3
replies
382
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 4 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
O.rka
▴ 710
1
vote
3
replies
374
views
PCA plot
DESeq2
PCAplot
updated 4 days ago by
LauferVA
4.2k • written 8 days ago by
Aaliya
▴ 10
1
vote
1
reply
216
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 2 days ago by
Ram
43k • written 2 days ago by
Jonathan Yoou
▴ 60
1
vote
1
reply
135
views
Two references 1. genome 2. plasmid for bowtie2
WGS
BacterialGenomics
Alignment
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Ruqaiya
• 0
1
vote
2
replies
117
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
11 hours ago by
Maverick
▴ 10
1
vote
3
replies
142
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 11 hours ago by
jared.andrews07
★ 16k • written 15 hours ago by
yvonneh
▴ 10
1
vote
1
reply
163
views
Including plasmid in alignment
Bacteria
Transcriptomics
BOWTIE2
STAR
2 days ago by
heelpPlease
• 0
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 11 hours ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
1
vote
7
replies
487
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 3 days ago by
bk11
★ 2.4k • written 7 days ago by
starswillfade
▴ 10
1
vote
2
replies
123
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
just now by
alifafiq1
• 0
1
vote
3
replies
259
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 2 days ago by
GenoMax
142k • written 2 days ago by
jeffrey.maurer.informatics
• 0
1
vote
3
replies
136
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 5 hours ago by
Alex Reynolds
35k • written 12 hours ago by
SJP
• 0
1
vote
2
replies
333
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
5 days ago by
Francesco
▴ 10
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 3 days ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
1
vote
3
replies
296
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Francesco
▴ 10
1
vote
7
replies
490
views
gvcf joint calling
WES
GATK
VCF
gVCF
4 days ago by
zihanss
• 0
1
vote
4
replies
386
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
3 days ago by
hagl
▴ 10
1
vote
4
replies
1.0k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
18 hours ago by
eesiribloom
▴ 80
1
vote
1
reply
117
views
Super ehancers
enhancers
updated 16 hours ago by
jared.andrews07
★ 16k • written 21 hours ago by
Oburah
• 0
1
vote
1
reply
112
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 16 hours ago by
bk11
★ 2.4k • written 1 day ago by
Jeol
▴ 20
1
vote
2
replies
235
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 16 hours ago by
Ram
43k • written 17 days ago by
eesiribloom
▴ 80
0
votes
1
reply
251
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 1 day ago by
Scooter
▴ 280 • written 7 days ago by
avocado123
• 0
0
votes
0
replies
74
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
1 day ago by
Vijith
▴ 30
0
votes
0
replies
65
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
23 hours ago by
Rhiannon
• 0
0
votes
0
replies
66
views
Use of annotation of integrated Seurat object in single sample
Seurat
21 hours ago by
Bine
▴ 60
0
votes
1
reply
190
views
Subsetting and merging back Seurat Object brings different results
Seurat
19 hours ago by
Bine
▴ 60
0
votes
6
replies
353
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
updated 17 hours ago by
GenoMax
142k • written 22 days ago by
eesiribloom
▴ 80
0
votes
4
replies
161
views
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 16 hours ago by
jared.andrews07
★ 16k • written 17 hours ago by
JH
• 0
0
votes
0
replies
70
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 16 hours ago by
Ram
43k • written 22 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
94
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 16 hours ago by
Ram
43k • written 22 hours ago by
4r-rtg
• 0
0
votes
1
reply
764
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 16 hours ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
452
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 16 hours ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
2
replies
126
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
14 hours ago by
Chen
• 0
0
votes
1
reply
113
views
RNA-seq data for deep learning classification
rna-seq
updated 14 hours ago by
dsull
★ 5.9k • written 16 hours ago by
Yuju
• 0
0
votes
1
reply
109
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 13 hours ago by
Ram
43k • written 1 day ago by
nithya
• 0
0
votes
2
replies
103
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
13 hours ago by
dtnondorf
• 0
0
votes
1
reply
92
views
Provean help
variant
Provean
updated 12 hours ago by
Mensur Dlakic
★ 27k • written 16 hours ago by
Arun Sai Kumar
• 0
0
votes
1
reply
93
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 11 hours ago by
anovak
▴ 120 • written 15 hours ago by
Hang
• 0
0
votes
0
replies
47
views
Empty table plot using plotGseaTable()
FGSEA
10 hours ago by
Chris
▴ 260
0
votes
7
replies
477
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 7 hours ago by
LChart
3.9k • written 3 days ago by
kl
▴ 10
0
votes
1
reply
120
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 5 hours ago by
Chris Dean
▴ 390 • written 14 hours ago by
sovrappensiero
▴ 90
0
votes
2
replies
631
views
homer not configured properly
Homer
makeTagDirectory
updated 4 hours ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
0
votes
1
reply
524
views
HOMER on AWS
HOMER
updated 4 hours ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
0
votes
0
replies
34
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
3 hours ago by
Jeyong
• 0
0
votes
0
replies
29
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
1 hour ago by
Vijith
▴ 30
0
votes
0
replies
15
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
1 hour ago by
Amos Bairoch
▴ 120
0
votes
5
replies
242
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 10 minutes ago by
Mohamed Abderrahmane
▴ 20 • written 3 days ago by
matteo.levorato
• 0
0
votes
3
replies
101
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 10 minutes ago by
ATpoint
82k • written 10 hours ago by
Qi
• 0
173 results • Page
2 of 4
Recent Votes
How to Calulate Allele Frequency from a VCF File?
Answer: allele frequency in VCF
Answer: Two references 1. genome 2. plasmid for bowtie2
A: Iterating through paired-end reads in samtools / pysam
Answer: Where Can I Download Some Bam Files?
Download SAM/BAM files from SRA takes ages!!!
Comment: Bedtools merge minimum overlap?
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Recent Replies
Comment: Does comparing two different groups to a common third group introduce bias in th
by
ATpoint
82k
Note that by basic algebra A vs C and B vs C is the same as A vs B, so you might rethink your analysis to answer your question in a much si…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
Yes, why not? If it works for you like that, bingo!
Answer: Does comparing two different groups to a common third group introduce bias in th
by
christopher medway
▴ 450
You are testing groups A and B to a common baseline (C) - I don't see that there is anything wrong with doing that. It is a fairly common a…
Comment: HOMER on AWS
by
clairechung112
• 0
Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
Answer: homer not configured properly
by
clairechung112
• 0
A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
Comment: Bedtools merge minimum overlap?
by
Alex Reynolds
35k
Note that, in place of `sort-bed - | uniq -`, you can pass the `--unique` option to `sort-bed`. The input is not strictly a BED6 file, but…
Comment: Post-imputation plot
by
LChart
3.9k
Imputation takes what? A day or two of compute time? Just re-do it.
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thanks. Really appreciate your help with this. This site is such a great resource. The methods aren't totally clear on how they're gettin…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
Comment: Does comparing two different groups to a common third group introduce bias in th
by
Qroid
▴ 40
Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
Answer: Bedtools merge minimum overlap?
by
harold.smith.tarheel
★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap?
by
bk11
★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
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