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116,563 results • Page
1 of 2332
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Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 1 minute ago by
GenoMax
141k • written 36 minutes ago by
Estevão
• 0
0
votes
2
replies
44
views
Difference between samtools "-f 9" and "-f 11"
samtools
sam
bam
19 minutes ago by
Dylan
• 0
0
votes
1
reply
26
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
updated 40 minutes ago by
Pierre Lindenbaum
161k • written 1 hour ago by
Lada
▴ 30
3
votes
10
replies
292
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 40 minutes ago by
Ram
43k • written 17 hours ago by
dominickd
• 0
3
votes
7
replies
294
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated just now by
bk11
★ 2.3k • written 6 weeks ago by
Sofia
• 0
0
votes
0
replies
21
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
2 hours ago by
ohtang7
▴ 40
0
votes
0
replies
29
views
How to merge UMAP coordinates with the concatenated loom files in anndata object
RNA-velocity
scanpy
loomfile
scvelo
python
2 hours ago by
Kash
▴ 110
2
votes
0
replies
43
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 3 hours ago by
Ram
43k • written 3 hours ago by
carlopecoraro2
★ 2.5k
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
2
votes
2
replies
344
views
Using vg gamsort with naive sorting algorithm
gamsort
vg
updated 4 hours ago by
Pierre Lindenbaum
161k • written 8 months ago by
AshleeThomson
▴ 80
0
votes
1
reply
70
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 5 hours ago by
GenoMax
141k • written 5 hours ago by
Srinka
▴ 20
8
votes
5
replies
4.6k
views
ISCN annotation for SV/CN VCF files
SV
written 7 months ago by
a.beggs
▴ 60
0
votes
4
replies
148
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 3 hours ago by
GenoMax
141k • written 5 hours ago by
njornet
▴ 20
5
votes
3
replies
517
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 6 hours ago by
colindaven
6.4k • written 5 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
37
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 3 hours ago by
Ram
43k • written 6 hours ago by
SHREYA
• 0
0
votes
3
replies
310
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
updated 6 hours ago by
colindaven
6.4k • written 8 days ago by
rj.rezwan
• 0
0
votes
0
replies
42
views
Merging replicates from Encode project
CHIP-seq
encode
6 hours ago by
Nurken
• 0
1
vote
3
replies
137
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
7 hours ago by
WouterDeCoster
47k
0
votes
3
replies
140
views
Help for coding: Trinity for differential gene expression studies
Gene
updated 5 hours ago by
mchour
• 0 • written 8 hours ago by
rhossen
• 0
1
vote
1
reply
98
views
WGCNA preservation analysis
WGCNA
preservation
updated 8 hours ago by
Michael
54k • written 9 hours ago by
michael.flower.14
▴ 180
0
votes
2
replies
110
views
some error in building kraken2 database
metagenome
kraken2
updated 3 hours ago by
Ram
43k • written 8 hours ago by
Art1ess
• 0
0
votes
1
reply
69
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 3 hours ago by
bk11
★ 2.3k • written 9 hours ago by
Susmita Mandal
▴ 110
0
votes
1
reply
79
views
Plots for DNA methylation data
plots
DNA
methylation
updated 6 hours ago by
GenoMax
141k • written 10 hours ago by
sarahawan92
▴ 10
0
votes
3
replies
439
views
python file for coding potential calculator
cpc2.py
updated 10 hours ago by
atharvakarkare14
▴ 10 • written 4 days ago by
Ashok
• 0
1
vote
1
reply
109
views
Failed kmer content
kmer
illumina
ngs
updated 3 hours ago by
Ram
43k • written 11 hours ago by
Kasturi
• 0
0
votes
1
reply
103
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 10 hours ago by
Basti
★ 2.0k • written 12 hours ago by
qudrat.nii
▴ 10
0
votes
0
replies
76
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
13 hours ago by
yxwucq
• 0
0
votes
0
replies
59
views
Seurat merge and batch correction
Seurat
14 hours ago by
sooni
▴ 20
0
votes
0
replies
45
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 2 hours ago by
Ram
43k • written 14 hours ago by
SSSJec
• 0
0
votes
5
replies
204
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
updated 18 hours ago by
Pierre Lindenbaum
161k • written 21 hours ago by
Sd
• 0
0
votes
2
replies
134
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
21 hours ago by
sainavyav22
• 0
0
votes
1
reply
102
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 22 hours ago by
Ram
43k • written 22 hours ago by
Cameron.walker9900
• 0
0
votes
8
replies
234
views
Error in cnetplot enrichplot package
R
updated 21 hours ago by
Ram
43k • written 23 hours ago by
Farhad
• 0
1
vote
4
replies
167
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 23 hours ago by
Mensur Dlakic
★ 27k • written 23 hours ago by
Κοσμάς
• 0
0
votes
0
replies
77
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 23 hours ago by
Ram
43k • written 23 hours ago by
maxime.policarpo
▴ 200
3
votes
3
replies
141
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 23 hours ago by
Mensur Dlakic
★ 27k • written 23 hours ago by
c_u
▴ 520
0
votes
0
replies
64
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 23 hours ago by
Ram
43k • written 23 hours ago by
sansan_96
▴ 80
0
votes
2
replies
122
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
22 hours ago by
dxj294
• 0
0
votes
0
replies
70
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 3 hours ago by
Ram
43k • written 23 hours ago by
Amélie
• 0
0
votes
0
replies
108
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 23 hours ago by
Ram
43k • written 1 day ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 21 hours ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
1
reply
112
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 1 day ago by
ATpoint
81k • written 1 day ago by
catherine.teyssier
• 0
2
votes
3
replies
160
views
from row count to tpm
tpm
row-count
normalization
10 hours ago by
michelafrancesconi9
▴ 20
0
votes
0
replies
72
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Abeer
• 0
1
vote
4
replies
171
views
Downsampling fastq file
downsample
fastq
updated 1 day ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 80
2
votes
3
replies
298
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 1 day ago by
dsull
★ 5.8k • written 14 days ago by
javanokendo
▴ 60
0
votes
1
reply
113
views
tbtool
tbtool
updated 1 day ago by
Ram
43k • written 1 day ago by
Raman
• 0
0
votes
2
replies
164
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Patadu94
• 0
3
votes
3
replies
186
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Mariana
▴ 10
0
votes
2
replies
136
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 23 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
emmanouil.a
▴ 120
116,563 results • Page
1 of 2332
Recent Votes
RNA-seq power estimation using ssizeRNA program
Answer: WGCNA preservation analysis
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
ISCN annotation for SV/CN VCF files
Comment: How to convert plink files to Hapmap Format
Am I crazy, or are most published RNA-seq studies vastly underpowered?
Trimming sequences based on NCBI contamination screen report
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AdviceSeeker
• 0
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Ann
★ 2.4k
Scholar
to
marco.barr
▴ 80
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Kash
▴ 110
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141k
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Recent Replies
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Ok. First update your phenotypes because in the 6th column all the values are -9 meaning missing, and then run `--assoc`. You can do the fo…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
i.sudbery
19k
You'll probably get away with using one of the other analysis pipelines, like Alevin-fry with much less than 128GB of RAM. Workstations can…
Comment: Difference between samtools "-f 9" and "-f 11"
by
Dylan
• 0
> (which is weird, if it's in proper pair, read and its mate should be both mapped) So that was my thought as well, I think the code you l…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
Ram
43k
> several single cell samples At the same time? You need a server, not a PC. Google around (and search the site as well with keyword "conf…
Answer: Difference between samtools "-f 9" and "-f 11"
by
Pierre Lindenbaum
161k
9: read must be paired AND mate must be unmapped 11: read must be paired AND mapped in proper pair AND mate must be unmapped (which is w…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
the data is binary and associated with a disease but we're studying only the cases and there are other phenotypes of severity
Comment: Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Ser
by
atowns21
• 0
could you share an example command of using STARSolo for the alignment? Did you use the json file directly? Or do you have to re-format the…
Comment: How to trim transcripts using information from NCBI contamination screen report
by
GenoMax
141k
> I didn't do a good job with Trimmomatic for some reason so I have to do some trimming of my transcripts. If you had extraneous sequence…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
Please answer my above question. What type of data is it, binary (cases and controls) or quantitative? You need to update Phenotype info in…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
This is how my .fam file looks like ![enter image description here][1] [1]: /media/images/caccd97c-3606-48d2-aa32-423a9882 And I run …
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.3k
What type of phenotype is in your data? It looks like it does not have affection status (default values for affection status will be: 1 = u…
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Agree. This is also a great solution that flips the problem on its head, as it were, Dominick. I dont want to be preachy, but this is why i…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
> linked to a list of grants Using [**EntrezDirect**][1] this may be much simpler if you have the grant number available. I tested this w…
Answer: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
Hi Dominick, One thing I am not sure of is, how is it that you got the other PMID in the first place? The reason I ask is that you mentio…
Comment: How to convert plink files to Hapmap Format
by
Sofia
• 0
Thanks Marco, btw do you have any idea why I get this "Warning: Skipping --assoc/--model since less than two phenotypes are present." aft…
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