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249 results • Page
3 of 5
Sort: Views
Rank
Views
Votes
Replies
3
votes
3
replies
462
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 5 days ago by
swbarnes2
14k • written 6 days ago by
joe
▴ 510
7
votes
6
replies
450
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
3 days ago by
analyst
▴ 30
2
votes
5
replies
428
views
Marking duplicates using UMIs
Deduplication
UMI
updated 2 days ago by
i.sudbery
19k • written 4 days ago by
Lipika
• 0
0
votes
6
replies
423
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 22 hours ago by
gv
• 0 • written 23 days ago by
Srinka
▴ 20
3
votes
4
replies
421
views
biomaRt error for different R version
biomaRt
R
updated 6 days ago by
GenoMax
141k • written 7 days ago by
manaswwm
▴ 490
0
votes
2
replies
417
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
5 days ago by
_quantum_girl_
▴ 10
1
vote
1
reply
410
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 6 days ago by
Chris
▴ 260
0
votes
2
replies
410
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
6 days ago by
Ashok
• 0
1
vote
1
reply
409
views
Plink merge errors.
cygwin64
bed
PLINK
5 days ago by
Dinmukhamed
• 0
2
votes
2
replies
409
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 1 day ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
2
votes
3
replies
407
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
6 days ago by
valentinatsar
• 0
1
vote
4
replies
402
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 1 day ago by
atowns21
• 0 • written 5 months ago by
ara
• 0
0
votes
1
reply
398
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 6 days ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
3
votes
9
replies
388
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 18 hours ago by
Istvan Albert
100k • written 2 days ago by
Κοσμάς
• 0
1
vote
1
reply
388
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow
python-apollo
Apollo
5 days ago by
renan.igor
• 0
3
votes
8
replies
376
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 2 hours ago by
swbarnes2
14k • written 1 day ago by
Aaliya
▴ 10
0
votes
2
replies
371
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
6 days ago by
Ashok
• 0
2
votes
2
replies
371
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
6 days ago by
nhaus
▴ 300
1
vote
1
reply
367
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
6 days ago by
otieno43
▴ 30
0
votes
10
replies
363
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
0
votes
3
replies
359
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 1 day ago by
colindaven
6.4k • written 10 days ago by
rj.rezwan
• 0
0
votes
2
replies
340
views
How to add motifs in cellranger-arc reference?
gtf
scRNAseq
fasta
cellranger
updated 6 days ago by
Ehsan
• 0 • written 9 weeks ago by
bioinfo
▴ 150
4
votes
2
replies
311
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 6 days ago by
Juke34
8.5k • written 6 days ago by
njornet
▴ 20
0
votes
2
replies
311
views
GSEA analysis in R
GSEA
R
Arabidopsis
6 days ago by
Sudip
• 0
2
votes
3
replies
304
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 2 days ago by
dsull
★ 5.8k • written 15 days ago by
javanokendo
▴ 60
1
vote
5
replies
298
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
1 day ago by
anasjamshed
▴ 120
1
vote
1
reply
293
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 5 days ago by
Ram
43k • written 5 days ago by
Nina
• 0
4
votes
6
replies
291
views
To get p-values for the TPM
P-value
TPM
RSEM
1 hour ago by
VITALA
• 0
2
votes
1
reply
281
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 5 days ago by
GenoMax
141k • written 5 days ago by
rebecca.calvo
• 0
0
votes
6
replies
280
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
1 day ago by
Sd
• 0
0
votes
8
replies
280
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Farhad
• 0
0
votes
1
reply
279
views
Could you please assist in identifying this cluster?
single-cell
updated 5 days ago by
Ram
43k • written 5 days ago by
Kazo
• 0
0
votes
0
replies
273
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 2 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
0
votes
5
replies
273
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
20 hours ago by
njornet
▴ 20
2
votes
4
replies
272
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
1 day ago by
HyperEvo
• 0
0
votes
1
reply
264
views
DEseq2
RNA-seq
DESeq2
updated 6 days ago by
Ram
43k • written 6 days ago by
rrehimi
• 0
0
votes
1
reply
264
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 6 days ago by
GenoMax
141k • written 6 days ago by
predeus
★ 1.9k
3
votes
2
replies
261
views
p-value and Boneferroni adjusted p-value the same in R
Bonferroni
R
Statistics
p-value
Fisher
2 days ago by
kristiewyleung
• 0
0
votes
1
reply
259
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 5 days ago by
GenoMax
141k • written 5 days ago by
bioyas
▴ 10
0
votes
4
replies
253
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
dxj294
• 0
1
vote
1
reply
253
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 4 days ago by
Gordon Smyth
★ 7.0k • written 5 days ago by
Bioinformatician
• 0
0
votes
2
replies
252
views
bam merging for archaic samples
samtools
bam
updated 3 days ago by
Ram
43k • written 4 days ago by
Matteo Ungaro
▴ 100
1
vote
5
replies
243
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
3
votes
5
replies
240
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 2 days ago by
GenoMax
141k • written 3 days ago by
ahmad.sajad4541
• 0
2
votes
4
replies
239
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
23 hours ago by
samuelkalandarov2002
▴ 10
7
votes
2
replies
231
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 390 • written 2 days ago by
catherine.teyssier
• 0
0
votes
3
replies
230
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 5 hours ago by
Kevin Blighe
87k • written 2 days ago by
qudrat.nii
▴ 10
1
vote
3
replies
228
views
some error in building kraken2 database
metagenome
kraken2
1 day ago by
Art1ess
• 0
1
vote
2
replies
226
views
permutation test in edgeR
rna-seq
edgeR
updated 3 days ago by
Gordon Smyth
★ 7.0k • written 16 days ago by
Netanel
• 0
1
vote
4
replies
219
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 14 hours ago by
GenoMax
141k • written 1 day ago by
Lada
▴ 30
249 results • Page
3 of 5
Recent Votes
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
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Recent Replies
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
b.contreras.moreira
▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM
by
VITALA
• 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
Comment: alignment result
by
ahmad.sajad4541
• 0
Thank you so much. Should i proceed for annotation step?
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
Answer: Network Alignment
by
Scooter
▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host
by
ZhangYuanfeng
• 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed)
by
Aaliya
▴ 10
I have actually used DESeq2 data.
Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
Dateline
• 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq
by
Kevin Blighe
87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies
by
Kevin Blighe
87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
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