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120,897 results • Page
1 of 2418
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Votes
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0
votes
1
reply
84
views
Error in importing data from 10x genomics into RStudio
H5
file
scRNA
RStudio
updated 7 hours ago by
GenoMax
150k • written 9 hours ago by
himanshu0102
• 0
1
vote
1
reply
97
views
Merge and unique multiple complete sam files from identical fastq files
samtools
aligment
sambamba
WGBS
WGS
updated 15 hours ago by
Pierre Lindenbaum
165k • written 16 hours ago by
JustinZhang
▴ 120
0
votes
1
reply
426
views
Issues with T2T in pigeon prepare from isoseq
isoseq
long
rna-seq
read
updated 1 day ago by
anbayega
• 0 • written 6 months ago by
SethJ
• 0
1
vote
1
reply
186
views
How to obtain TPM data after batch effect correction from count data obtained using RSEM
STAR
RNA-seq
Batch
RSEM
effect
updated 1 day ago by
Gordon Smyth
★ 7.9k • written 1 day ago by
Apprentice
▴ 170
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
1
vote
1
reply
259
views
Missing short indels from vcf
bcftools
shortindels
mpileup
updated 1 day ago by
LauferVA
4.7k • written 4 days ago by
kbranger
• 0
4
votes
6
replies
396
views
Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
updated 1 day ago by
mmhryc
• 0 • written 3 days ago by
harsh
▴ 20
1
vote
2
replies
179
views
Choosing the best clustering method for a certain methylation data
DMR
k-means
hierarchical
clustering
methylation
updated 1 day ago by
5heikki
11k • written 1 day ago by
Sophia
• 0
3
votes
5
replies
293
views
Extract length of sample sequence from vcf
microsatellites
bcftools
vcf
indels
variants
updated 1 day ago by
Billy Rowell
▴ 500 • written 1 day ago by
jahnreinhard.ringger
• 0
1
vote
12
replies
408
views
MultiQC_report
content_multiqc_fastqc
Quality_control_
Adapter
updated 1 day ago by
GenoMax
150k • written 1 day ago by
AIMAR
• 0
2
votes
2
replies
197
views
Forum:
How to get into research for an absolute beginners
research
updated 1 day ago by
GenoMax
150k • written 1 day ago by
jpeduprep
• 0
0
votes
0
replies
101
views
News:
Online course — Comparative Genomics — 7–11 April
SNVs
ComparativeGenomics
SVs
GenomeAnnotation
1 day ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
175
views
how to do a corellation analysis of multiple CRISPR data sets
batch-effect.
crispr
screen
correlation
1 day ago by
Assa Yeroslaviz
★ 1.9k
8
votes
4
replies
403
views
Alternatives to UCSC genome browser for obtaining gene coordinates
browser
ucsc
updated 1 day ago by
LauferVA
4.7k • written 4 days ago by
shpak.max
▴ 60
1
vote
9
replies
409
views
Tool:
Introducing Grantease: Go From RFA to First Draft Grant Proposal in 15 Minutes
ai
biology
grants
nih
litreview
updated 1 day ago by
jared.andrews07
★ 18k • written 2 days ago by
Will
• 0
0
votes
0
replies
139
views
Job:
Postdoctoral Position in Computational Protein Design and Molecular Modelling
opportunity
postdoc
2 days ago by
Sophie
• 0
1
vote
3
replies
263
views
Modify read groups in BAM file
samtools
BAM
picard
DRAGEN
updated 1 day ago by
1769mkc
★ 1.2k • written 2 days ago by
Alex
• 0
0
votes
1
reply
181
views
How to put distinct colors to connection bridges in the Sankey plot ?
R
Python
Sankey
updated 2 days ago by
zx8754
12k • written 2 days ago by
ohtang7
▴ 40
0
votes
0
replies
142
views
PCA comparison of cell line vs tumors
RNAseq
Sequencing
PCA
Normalization
2 days ago by
karlensberg
• 0
0
votes
9
replies
452
views
Find the reads which correspond to DP of vcf
bam
variant
vcf
sam2tsv
updated 2 days ago by
Pierre Lindenbaum
165k • written 3 days ago by
totoroGirl
• 0
1
vote
1
reply
207
views
cibersortx error - $ operator is invalid for atomic vectors
cibersortx
2 days ago by
Franck
• 0
0
votes
0
replies
129
views
Need help defining a threshold
DAVID
Genes
GO
2 days ago by
Ana
• 0
5
votes
9
replies
510
views
Larger genome size than expected-please help
genome
nanopore
size
minimap2
updated 2 days ago by
colindaven
7.3k • written 3 days ago by
alexandrakortsi
• 0
5
votes
4
replies
284
views
PCA plots in ATAC-seq replicates: Is it okay to use vst transformed data for visualization?
ATAC-seq
diffbind
updated 2 days ago by
ATpoint
87k • written 2 days ago by
maplewj
▴ 20
0
votes
1
reply
361
views
Question about `vg construct`
vg
updated 3 days ago by
Jouni Sirén
▴ 630 • written 8 days ago by
zhengluo
• 0
0
votes
0
replies
152
views
How can I use mcmcglmm to calculate whether two traits are correlated?
glmm
statistics
evolution
3 days ago by
雨
▴ 20
0
votes
2
replies
504
views
DiffBind normalization error: invalid argument type (list) - cannot make it work, everything seems correct
normalization
deseq2
chipseq
diffbind
2 days ago by
buffealo
▴ 130
1
vote
8
replies
1.6k
views
6 follow
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 3 days ago by
lieven.sterck
15k • written 12 months ago by
Matt
• 0
80
votes
32
replies
31k
views
18 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 1 day ago by
Paulo
▴ 10 • written 11.2 years ago by
Istvan Albert
102k
1
vote
4
replies
365
views
News:
Wolfram tech for bio data analysis
plots
statistics
databases
ai
3 days ago by
dk7258859
• 0
0
votes
1
reply
240
views
MULTIQC for miRNAseq data
multiqc
updated 3 days ago by
i.sudbery
21k • written 4 days ago by
Alana Conceição Maia Lessa
• 0
0
votes
1
reply
269
views
How to improve the mapping rate of vg giraffe
vg
updated 3 days ago by
colindaven
7.3k • written 4 days ago by
gulin
• 0
0
votes
6
replies
400
views
miRNA-seq normalization
miRDeep2
normalization
RNA-seq
miRNA-seq
miRNA
23 hours ago by
paulanavarrete116
• 0
2
votes
2
replies
335
views
Issues with vg surject into paths
vg
updated 3 days ago by
GenoMax
150k • written 4 days ago by
Rugare
• 0
8
votes
12
replies
563
views
Batch correction RNA-seq analysis
rna-seq
ComBat-seq
batch
correction
updated 4 days ago by
LauferVA
4.7k • written 4 days ago by
ka132
▴ 10
0
votes
3
replies
285
views
bbduk.sh trimming to BAM output file
bbduk.sh
updated 4 days ago by
GenoMax
150k • written 4 days ago by
bge
• 0
0
votes
2
replies
276
views
DEG analysys using pseudobulk from single cell RNA-seq
DEG
scRNA-seq
3 days ago by
Diego
▴ 110
1
vote
1
reply
216
views
Microarray platform probrID to Circ-ID problem
CircRNA
microarray
updated 4 days ago by
GenoMax
150k • written 4 days ago by
ParastooA
▴ 20
0
votes
4
replies
316
views
Checking sex of a sample with sequencing data
ATAC-seq
3 days ago by
xqyn
▴ 30
1
vote
5
replies
504
views
Depth in Cram file does not match depth in VCF file
IGV
of
Depth
SNV
coverage
updated 4 days ago by
Istvan Albert
102k • written 6 days ago by
shu8
• 0
1
vote
1
reply
231
views
Tools for clustering genes rather than samples for bulk RNA-seq
time
Bulk
RNA-seq
course
clustering
updated 4 days ago by
i.sudbery
21k • written 4 days ago by
ATS
• 0
2
votes
2
replies
386
views
what database should I use for de novo genome in AUGUSTUS
genome
AUGUSTUS
galaxy
annotation
updated 3 days ago by
lieven.sterck
15k • written 7 days ago by
Jl
• 0
1
vote
5
replies
357
views
Is there a tool to obtain GO terms for thousands of genes at once?
permutations
Genes
updated 1 day ago by
Istvan Albert
102k • written 4 days ago by
Ana
• 0
0
votes
1
reply
232
views
cant make the correct matrix
logfc
csv
updated 4 days ago by
lieven.sterck
15k • written 4 days ago by
Naila
• 0
1
vote
4
replies
313
views
FIxing Gene Models in Funannotate
genomics
funannotate
fungus
annotation
4 days ago by
SomeOne
▴ 170
1
vote
7
replies
410
views
How to Make Cell Order identical Between Two Seurat Objects in R?
R
seurat
scRNA-seq
updated 4 days ago by
yura.grabovska
▴ 760 • written 4 days ago by
zhang616123
• 0
0
votes
3
replies
305
views
Assign different color in same section of Chord diagram in R
Chart
R
Diagram
Plot
Chord
updated 4 days ago by
Bastien Hervé
6.2k • written 4 days ago by
Jonathan Yoou
▴ 70
0
votes
0
replies
197
views
News:
Live Online course: Introduction to Python, April, 2025
python
programming
course
4 days ago by
soledad.esteban
• 0
0
votes
4
replies
318
views
Niormalization process in creating heatmap
Z
heatmap
score
Normalization
updated 5 days ago by
ATpoint
87k • written 5 days ago by
ZuelTech
• 0
1
vote
14
replies
726
views
Lacking exons in gtf file of a virus' genome
gtf
exon
Mapping
Hazara
VirusGenome
updated 5 days ago by
colindaven
7.3k • written 5 days ago by
ZuelTech
• 0
120,897 results • Page
1 of 2418
Recent Votes
Answer: How to obtain TPM data after batch effect correction from count data obtained us
Answer: Merge and unique multiple complete sam files from identical fastq files
Comment: MultiQC_report
Answer: Missing short indels from vcf
Answer: Extract length of sample sequence from vcf
Answer: Extract length of sample sequence from vcf
Answer: Modify read groups in BAM file
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Recent Replies
Comment: Error in importing data from 10x genomics into RStudio
by
GenoMax
150k
Please post exact code/packages you are using. It is unclear what you are doing at this time.
Answer: Merge and unique multiple complete sam files from identical fastq files
by
Pierre Lindenbaum
165k
I wrote https://jvarkit.readthedocs.io/en/latest/SamRemoveDuplicatedNames/ this program just remove the duplicated name+flag but doesn't l…
Comment: miRNA-seq normalization
by
paulanavarrete116
• 0
I'm not sure about your question. The 3' adapters were removed in the first step of the workflow using miRDeep2 mapper which allows for rem…
Comment: Issues with T2T in pigeon prepare from isoseq
by
anbayega
• 0
Got the same error using T2T. I will wait to see if there's a quick fix.
Comment: Extract length of sample sequence from vcf
by
Billy Rowell
▴ 500
If you don't want to mess with compiling bleeding-edge bcftools, you could write the same thing in awk. There's no need to filter out the …
Answer: How to obtain TPM data after batch effect correction from count data obtained us
by
Gordon Smyth
★ 7.9k
I would be using divided counts for transcript-level analyses from RSEM, and using log-CPM from the divided counts for clustering, for the …
Answer: Missing short indels from vcf
by
LauferVA
4.7k
Hey @kbranger , IIUC, you have a ~7 bp deletion visible in IGV (with a 7D CIGAR string and ~17–20× depth) that disappears after bcftools…
Comment: Modify read groups in BAM file
by
1769mkc
★ 1.2k
is this onboard or basespace or ICA? dragen
Comment: MultiQC_report
by
GenoMax
150k
That is pretty odd. Like you were advised above you could try to open an issue with the devs. I don't think I have ever seen this problem. …
Answer: Facing issue with output of nextflow pipeline
by
mmhryc
• 0
With nextflow you don't want to manage paths manually. Instead of creating a hardcoded path you should let it output the results into whate…
Answer: Choosing the best clustering method for a certain methylation data
by
5heikki
11k
[Affinity propagation][1] is the answer to all my clustering needs [1]: https://utstat.toronto.edu/reid/sta414/frey-affinity.pdf
Comment: Modify read groups in BAM file
by
Alex
• 0
Thanks Istvan, this seems like a reasonable enough solution that could be scripted across large batches of files. I'll give it a shot. Was …
Comment: MultiQC_report
by
AIMAR
• 0
No I don't, when I said errors I mean it shows 267 samples for the adapter content while I just have 50 samples of paired-end read = 100 re…
Comment: MultiQC_report
by
GenoMax
150k
> in this report multiqc missed 3 samples (6 reports ) and still made the error with the adapter content. Do you have any oddities in samp…
Answer: Extract length of sample sequence from vcf
by
Billy Rowell
▴ 500
This is hacky and definitely not prod ready, but if the goal is to get the length and not the sequence, you could use bcftools/paste/bc to …
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