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120,883 results • Page
1 of 2418
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0
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How can I use mcmcglmm to calculate whether two traits are correlated?
glmm
statistics
evolution
just now by
雨
▴ 20
0
votes
1
reply
65
views
DiffBind normalization error: invalid argument type (list) - cannot make it work, everything seems correct
normalization
deseq2
chipseq
diffbind
updated 53 minutes ago by
Rory Stark
★ 2.1k • written 6 hours ago by
buffealo
▴ 130
1
vote
5
replies
1.3k
views
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated just now by
GenoMax
150k • written 12 months ago by
Matt
• 0
77
votes
30
replies
31k
views
18 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 hours ago by
Paulo
• 0 • written 11.1 years ago by
Istvan Albert
102k
0
votes
4
replies
114
views
Larger genome size than expected-please help
genome
nanopore
size
minimap2
updated 5 hours ago by
GenoMax
150k • written 6 hours ago by
alexandrakortsi
• 0
0
votes
0
replies
45
views
cibersortx error - $ operator is invalid for atomic vectors
cibersortx
4 hours ago by
Franck
• 0
1
vote
4
replies
200
views
News:
Wolfram tech for bio data analysis
plots
statistics
databases
ai
7 hours ago by
dk7258859
• 0
835
votes
169
replies
172k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
0
votes
7
replies
131
views
Find the reads which correspond to DP of vcf
bam
variant
vcf
sam2tsv
2 hours ago by
totoroGirl
• 0
1
vote
5
replies
131
views
Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
updated 7 hours ago by
colindaven
7.3k • written 8 hours ago by
harsh
• 0
0
votes
1
reply
107
views
MULTIQC for miRNAseq data
multiqc
updated 12 hours ago by
i.sudbery
21k • written 1 day ago by
Alana Conceição Maia Lessa
• 0
0
votes
1
reply
103
views
How to improve the mapping rate of vg giraffe
vg
updated 12 hours ago by
colindaven
7.3k • written 19 hours ago by
gulin
• 0
0
votes
5
replies
164
views
miRNA-seq normalization
miRDeep2
normalization
RNA-seq
miRNA-seq
miRNA
updated 9 hours ago by
GenoMax
150k • written 14 hours ago by
paulanavarrete116
• 0
2
votes
2
replies
185
views
Issues with vg surject into paths
vg
updated 11 hours ago by
GenoMax
150k • written 1 day ago by
Rugare
• 0
0
votes
0
replies
82
views
Missing short indels from vcf
bcftools
shortindels
mpileup
22 hours ago by
kbranger
• 0
8
votes
12
replies
310
views
Batch correction RNA-seq analysis
rna-seq
ComBat-seq
batch
correction
updated 13 hours ago by
LauferVA
4.6k • written 1 day ago by
ka132
▴ 10
0
votes
3
replies
134
views
bbduk.sh trimming to BAM output file
bbduk.sh
updated 23 hours ago by
GenoMax
150k • written 1 day ago by
bge
• 0
1
vote
1
reply
108
views
Alternatives to UCSC genome browser for obtaining gene coordinates
browser
ucsc
updated 23 hours ago by
GenoMax
150k • written 1 day ago by
shpak.max
▴ 50
0
votes
2
replies
136
views
DEG analysys using pseudobulk from single cell RNA-seq
DEG
scRNA-seq
10 hours ago by
Diego
▴ 110
1
vote
1
reply
85
views
Microarray platform probrID to Circ-ID problem
CircRNA
microarray
updated 1 day ago by
GenoMax
150k • written 1 day ago by
ParastooA
▴ 20
0
votes
1
reply
100
views
Checking sex of a sample with sequencing data
ATAC-seq
updated 10 hours ago by
ATpoint
87k • written 1 day ago by
xqyn
▴ 30
1
vote
5
replies
333
views
Depth in Cram file does not match depth in VCF file
IGV
of
Depth
SNV
coverage
updated 1 day ago by
Istvan Albert
102k • written 3 days ago by
shu8
• 0
1
vote
1
reply
105
views
Tools for clustering genes rather than samples for bulk RNA-seq
time
Bulk
RNA-seq
course
clustering
updated 1 day ago by
i.sudbery
21k • written 1 day ago by
ATS
• 0
0
votes
1
reply
211
views
what database should I use for de novo genome in AUGUSTUS
genome
AUGUSTUS
galaxy
annotation
updated 1 day ago by
lieven.sterck
15k • written 3 days ago by
Jl
• 0
1
vote
3
replies
144
views
Is there a tool to obtain GO terms for thousands of genes at once?
permutations
Genes
updated 1 day ago by
GenoMax
150k • written 1 day ago by
Ana
• 0
0
votes
1
reply
112
views
cant make the correct matrix
logfc
csv
updated 1 day ago by
lieven.sterck
15k • written 1 day ago by
Naila
• 0
1
vote
4
replies
155
views
FIxing Gene Models in Funannotate
genomics
funannotate
fungus
annotation
1 day ago by
SomeOne
▴ 170
1
vote
7
replies
223
views
How to Make Cell Order identical Between Two Seurat Objects in R?
R
seurat
scRNA-seq
updated 1 day ago by
yura.grabovska
▴ 750 • written 1 day ago by
zhang616123
• 0
0
votes
3
replies
168
views
Assign different color in same section of Chord diagram in R
Chart
R
Diagram
Plot
Chord
updated 14 hours ago by
Bastien Hervé
6.2k • written 1 day ago by
Jonathan Yoou
▴ 70
0
votes
0
replies
88
views
News:
Live Online course: Introduction to Python, April, 2025
python
programming
course
1 day ago by
soledad.esteban
• 0
0
votes
4
replies
165
views
Niormalization process in creating heatmap
Z
heatmap
score
Normalization
updated 1 day ago by
ATpoint
87k • written 1 day ago by
ZuelTech
• 0
1
vote
14
replies
476
views
Lacking exons in gtf file of a virus' genome
gtf
exon
Mapping
Hazara
VirusGenome
updated 1 day ago by
colindaven
7.3k • written 2 days ago by
ZuelTech
• 0
1
vote
4
replies
1.0k
views
Should I process two complete sets of 10x single-cell multiomics sequencing files from one donor together or separately?
10x_multiome
ENCODE
cellranger_arc
updated 1 day ago by
swbarnes2
14k • written 3 days ago by
Wu-Sheng Zhang
• 0
1
vote
4
replies
233
views
Count matrices plotting
count
matrix
scanpy
1 day ago by
NIkita
• 0
3
votes
8
replies
263
views
Filter snRNA-seq .fastq files based on barcodes
snRNA-seq
scRNA-seq
FASTQ
bbmap
updated 1 day ago by
GenoMax
150k • written 1 day ago by
connorjfausto
▴ 30
0
votes
1
reply
157
views
Defining Sex Chromosomes in PLINK for a Camel Genome
plink
vcf
updated 2 days ago by
chrchang523
11k • written 2 days ago by
Smilesky
• 0
0
votes
0
replies
98
views
Why is the IC50 of the low-risk group always lower than that of the high-risk group?
OncoPredict
2 days ago by
nuorain
▴ 40
0
votes
0
replies
111
views
News:
Introduction to Epigenomics course
Epigenomics
RNA-seq
ATAC-seq
Chip-seq
HI-C
2 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
170
views
Remove batch effect RnaSeq (RUVg)
ruvg
batch
rnaseq
remove
1 day ago by
aLex97
• 0
0
votes
0
replies
116
views
Annotation of CpG, DMRs and DMPs with MethylKit and Genomation in R
dmp
methylkit
dmr
CpG
2 days ago by
egascon
▴ 60
1
vote
0
replies
206
views
Tool:
A rust binding for pairwise/multiple sequence aligner: bsalign-rs
bsalign
alignment
16 hours ago by
dwpeng
▴ 120
0
votes
2
replies
303
views
Perform DEGs with pyDESeq2 in CCLE Melanoma Data But Contains Negative Values
DEG
CCLE
Melanoma
pyDESeq2
4 days ago by
mete.han.celebi
• 0
0
votes
0
replies
202
views
energy minimisation
Energy
updated 4 days ago by
Pierre Lindenbaum
165k • written 4 days ago by
swarnadurga66666m
• 0
0
votes
1
reply
235
views
How to concatenate different domains in the target database identified by hmmsearch
multiple
domains
hmmsearch
updated 4 days ago by
GenoMax
150k • written 4 days ago by
Yongjie Zhang
▴ 110
0
votes
1
reply
244
views
How to filter Hmmsearch alignment
Hmmsearch
updated 4 days ago by
Mensur Dlakic
★ 29k • written 4 days ago by
Yongjie Zhang
▴ 110
2
votes
3
replies
2.3k
views
Defining residues as buried or exposed based in ASAs/RSAs
structural-bioinformatics
protein-biology
updated 4 days ago by
Dan A
• 0 • written 3.7 years ago by
Agenor Neto
▴ 10
1
vote
1
reply
265
views
Understanding Re-use of Query Sequences in Long Read Alignments
Alignment
PacBio
pbmm2
Minimap2
updated 4 days ago by
LauferVA
4.6k • written 4 days ago by
Charles-Alexandre Roy
▴ 50
0
votes
0
replies
199
views
Question about `vg construct`
vg
4 days ago by
zhengluo
• 0
0
votes
2
replies
341
views
Discrepancy between BAM and vcf
discrepancy
vcf
DRAGEN
updated 5 days ago by
Istvan Albert
102k • written 5 days ago by
louis-gil
• 0
2
votes
1
reply
457
views
Question about `vg giraffe`
vg
updated 5 days ago by
GenoMax
150k • written 6 days ago by
zhengluo
• 0
120,883 results • Page
1 of 2418
Recent Votes
Answer: Depth in Cram file does not match depth in VCF file
Comment: False heterozygosity at chromosome X for male sample in Exome Sequencing
Investigating male X heterozygosity in short read sequencing
Investigating male X heterozygosity in short read sequencing
Comment: Facing issue with output of nextflow pipeline
A: How to get 1 top hit only for each query in blastx
Answer: Alternatives to UCSC genome browser for obtaining gene coordinates
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Comment: FastQC on nanopore data: high proportion of polyA and polyG. Why ?
by
GenoMax
150k
Original question was about nanopore data. Are you referring to PacBio HiFi data?
Answer: DiffBind normalization error: invalid argument type (list) - cannot make it work
by
Rory Stark
★ 2.1k
If your peaks are in `narrowPeak` format, it may help to set the `PeakCaller` to `"narrow"`.
Comment: FastQC on nanopore data: high proportion of polyA and polyG. Why ?
by
vkaz
• 0
@Matt -- Hi, did you figure out about the cause of poly-A spike in your reads? I have similar problem in genomic HiFi reads.
Comment: Find the reads which correspond to DP of vcf
by
totoroGirl
• 0
Okay so I used the command which you mentioned earlier, since I only want the reads which have a G to T substitution, I parsed the output s…
Comment: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
by
Paulo
• 0
Hi Istvan! This was exactly what I was looking for! Amazing how 11 years after, this post is still usefull and active :) I have a que…
Comment: Larger genome size than expected-please help
by
GenoMax
150k
> The problem is that they all have many contigs (over 300) That may indicate that these may not be "complete/reference" quality. How many…
Answer: Larger genome size than expected-please help
by
Istvan Albert
102k
Genome assembly is still a trial and error process, but getting 39 million genomes for a 34-million-long expectation is not too bad. Oft…
Comment: Larger genome size than expected-please help
by
alexandrakortsi
• 0
Because it is a very common species and there are 15 available genomes around the size i mentioned. The problem is that they all have many …
Comment: Larger genome size than expected-please help
by
GenoMax
150k
> if these extra million bp are real (seems unlikely) Why do you feel that way? Have you aligned your assembly to an available reference…
Comment: Find the reads which correspond to DP of vcf
by
totoroGirl
• 0
yes! I am running it now but your second suggestion: samtools view in.bam "chrX:124068651-124068651" | cut -f1 will give me all the read…
Comment: Find the reads which correspond to DP of vcf
by
totoroGirl
• 0
jup you are right sorry the updated bed file looks like this: chrX 124068649 124068651 I then grep "124068651" res.txt > res_fil…
Comment: Find the reads which correspond to DP of vcf
by
Pierre Lindenbaum
165k
please try my samtools command above (fixed a few minutes ago, missing -h)
Comment: Find the reads which correspond to DP of vcf
by
Pierre Lindenbaum
165k
>reg.bed looks this way: chrX 124068651 124068651 it cannot work anyway, you should get an error message: [WARN][BedLineCodec]cannot use …
Comment: Find the reads which correspond to DP of vcf
by
totoroGirl
• 0
java -jar /mnt/beegfs/sbhattacharya/clone_tracing/bam_file/M1/jvarkit/dist/jvarkit.jar sam2tsv -R GCA_000001405.15_GRCh38_no_alt_analys…
Comment: Find the reads which correspond to DP of vcf
by
Pierre Lindenbaum
165k
> And there are such 18683080 entries. It is not possible to have so many entries because we have performed nest I wrote this tool, how di…
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