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116,876 results • Page
4 of 2338
Sort: Rank
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Votes
Replies
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
5 days ago by
Zhenyu Zhang
★ 1.2k
2
votes
1
reply
310
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 7 days ago by
chrchang523
10k • written 10 days ago by
8armed
▴ 10
0
votes
5
replies
354
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 7 days ago by
chrchang523
10k • written 7 days ago by
curious
▴ 750
0
votes
1
reply
216
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 6 days ago by
Ram
43k • written 7 days ago by
Rob
▴ 170
0
votes
2
replies
246
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 9 hours ago by
GenoMax
142k • written 7 days ago by
Ximena
• 0
0
votes
1
reply
202
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 6 days ago by
Ram
43k • written 7 days ago by
Valentina
• 0
0
votes
6
replies
435
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 7 days ago by
swbarnes2
14k • written 7 days ago by
Erina
• 0
0
votes
2
replies
237
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
4 days ago by
kalavattam
▴ 190
1
vote
3
replies
293
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
5 days ago by
Lada
▴ 30
1
vote
0
replies
151
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 4 days ago by
zx8754
11k • written 7 days ago by
Emilie
▴ 10
0
votes
0
replies
140
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
7 days ago by
Javier
• 0
0
votes
1
reply
238
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Thanujay S
• 0 • written 7 days ago by
yahn
• 0
0
votes
0
replies
132
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
7 days ago by
mikemakaveli1
• 0
2
votes
2
replies
221
views
Raw counts using stringtie
stringtie
RNA-seq
updated 7 days ago by
GenoMax
142k • written 7 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
134
views
Modify plot R mtDNA indel
plot
mtDNA
R
7 days ago by
marco.barr
▴ 100
0
votes
0
replies
324
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
7 days ago by
NorbertK
▴ 10
4
votes
2
replies
246
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 6 days ago by
Ram
43k • written 7 days ago by
carolofharvest
▴ 40
13
votes
14
replies
825
views
High Malat-1 expression in single cell data
single-cell
updated 2 days ago by
t.montserrat.ayuso
▴ 40 • written 11 days ago by
carolofharvest
▴ 40
0
votes
2
replies
256
views
Downloading older version of a tool
Alignment
tools
7 days ago by
Ruqaiya
• 0
0
votes
0
replies
149
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
7 days ago by
rustykb
▴ 20
1
vote
1
reply
193
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 6 days ago by
Ram
43k • written 7 days ago by
adi.gershon1
• 0
3
votes
5
replies
291
views
Generating mpileup file using samtools
mpileup
samtools
updated 7 days ago by
Joe
21k • written 7 days ago by
Ruqaiya
• 0
0
votes
5
replies
377
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 7 days ago by
b.contreras.moreira
▴ 180 • written 8 days ago by
JH
• 0
1
vote
3
replies
292
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 7 days ago by
ATpoint
82k • written 8 days ago by
Qi
• 0
0
votes
0
replies
140
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
7 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
296
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 7 days ago by
dthorbur
★ 1.9k • written 7 days ago by
Vijith
▴ 30
0
votes
0
replies
151
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
8 days ago by
Jeyong
• 0
0
votes
2
replies
734
views
homer not configured properly
Homer
makeTagDirectory
updated 8 days ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
283
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 8 days ago by
Alex Reynolds
35k • written 8 days ago by
SJP
• 0
0
votes
0
replies
137
views
Empty table plot using plotGseaTable()
FGSEA
7 days ago by
Chris
▴ 280
0
votes
1
reply
191
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 8 days ago by
anovak
▴ 120 • written 8 days ago by
Hang
• 0
1
vote
3
replies
245
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 8 days ago by
jared.andrews07
★ 16k • written 8 days ago by
yvonneh
▴ 10
3
votes
5
replies
348
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
7 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 8 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
209
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
8 days ago by
dtnondorf
• 0
3
votes
8
replies
619
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 4 days ago by
Chris Dean
▴ 410 • written 8 days ago by
sovrappensiero
▴ 100
1
vote
2
replies
248
views
RNA-seq data for deep learning classification
rna-seq
7 days ago by
yahn
• 0
3
votes
8
replies
532
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
4 days ago by
Qroid
▴ 40
0
votes
1
reply
526
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 8 days ago by
Hugo
• 0 • written 5 months ago by
Rachel
• 0
0
votes
1
reply
164
views
Provean help
variant
Provean
updated 8 days ago by
Mensur Dlakic
★ 27k • written 8 days ago by
Arun Sai Kumar
• 0
1
vote
1
reply
171
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 8 days ago by
bk11
★ 2.4k • written 8 days ago by
Jeol
▴ 20
1
vote
1
reply
179
views
Super ehancers
enhancers
updated 8 days ago by
jared.andrews07
★ 16k • written 8 days ago by
Oburah
• 0
0
votes
6
replies
317
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 7 days ago by
dsull
★ 6.0k • written 8 days ago by
Chen
• 0
5
votes
5
replies
292
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 8 days ago by
atharvakarkare14
▴ 30 • written 8 days ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
462
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
7 days ago by
eebloom
▴ 80
3
votes
3
replies
344
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 7 days ago by
ATpoint
82k • written 8 days ago by
alifafiq1
• 0
0
votes
0
replies
104
views
Use of annotation of integrated Seurat object in single sample
Seurat
8 days ago by
Bine
▴ 60
0
votes
0
replies
110
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 8 days ago by
Ram
43k • written 8 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
234
views
Subsetting and merging back Seurat Object brings different results
Seurat
8 days ago by
Bine
▴ 60
0
votes
0
replies
158
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 8 days ago by
Ram
43k • written 8 days ago by
4r-rtg
• 0
116,876 results • Page
4 of 2338
Recent Votes
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
Answer: what is another word for a BLAST "hit"?
Comment: what is another word for a BLAST "hit"?
Comment: what is another word for a BLAST "hit"?
Comment: How can I merge GFF files together to produce a file with gene functions from bo
Comment: Contig assembly task, errors
Comment: Where to get the following bed file?
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Recent Replies
Answer: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
use bcftools merge with --force-samples and then use jvarkit https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ to replace the no-call …
Answer: In IGV is this a heterogeneous mutation or false call?
by
swbarnes2
14k
Since all the reads that show the alternate allele have to be clipped to align there, I'd say those reads are misaligned. I would say that…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
> Here's a few lines from the head of the raw fastq If your files are actually compressed (as their names suggest) then you should not be …
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
GenoMax
142k
If you added the `\` before the `+` then there is no need for it. It makes it appear that the sequences are not in proper fastq format. Ple…
Comment: Tassel 5 GBS: Is there something wrong with my fastqs?
by
Mensur Dlakic
★ 27k
This seems to be the same unanswered question as before, except that its description is split over two threads. You are now forcing us to r…
Answer: what is another word for a BLAST "hit"?
by
dec986
▴ 380
I'll probably go with "matches" even though it doesn't sound as good as just "hit"
Comment: what is another word for a BLAST "hit"?
by
bk11
★ 2.4k
> hits from BLAST hits sequences
Comment: what is another word for a BLAST "hit"?
by
Pierre Lindenbaum
161k
> is there a synonym for hits from BLAST? alignment
Comment: How are score_weights calculated in this code?
by
Ram
43k
Is this ALL the context you can give us?
Comment: Genome Assembly task + Protein Translation, assignment advice on a question
by
Ram
43k
Where did you copy-paste this from? It looks like an assignment question.
Comment: Contig assembly task, errors
by
rackbersingh
• 0
Hi Phillip, Thanks for sharing you knowledge and funnily enough this really was an amplitude test, but anyways your sharing of knowledge h…
Comment: Can I readmap short reads to rDNA references?
by
GenoMax
142k
If these are short reads and the organisms are related then you are going to have a difficult time classifying the reads.
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142k
With a large dataset it is always best to do the search locally (or in the cloud, if you don't have necessary hardware available locally).
Comment: Truncated metadata file report from ENA Portal API
by
Giulia
• 0
Thank you so much for your hint! I'll look into this!
Comment: How to convert Haps file to vcf file?
by
curious
▴ 750
unzip haps then: bin/shapeit \ -convert \ --input-haps {haps_prefix} \ --thread {cpus} \ --output-…
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