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121,301 results • Page
1 of 2427
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Votes
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0
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0
replies
18
views
Merging single ATAC seq data sets from multiple sample
10x
1 hour ago by
1769mkc
★ 1.3k
0
votes
1
reply
47
views
GSEA analysis in R
R
ranked_list
GSEA
updated 1 hour ago by
ATpoint
88k • written 3 hours ago by
rajdeepboral00
▴ 70
0
votes
1
reply
52
views
ATAC-seq analysis
ATAC-seq
Samtools
Sorting
updated 3 hours ago by
GenoMax
151k • written 3 hours ago by
SEJAL
• 0
0
votes
1
reply
67
views
Assembly issues
adapters
Assembly
Spades
updated 5 hours ago by
GenoMax
151k • written 5 hours ago by
anna
• 0
1
vote
6
replies
258
views
Use taxdb tp get scientific names in local BLAST output
taxdb
sscinames
taxonomy
makeblastdb
blast
updated 3 hours ago by
GenoMax
151k • written 1 day ago by
Luca Arbore
▴ 10
838
votes
170
replies
178k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 weeks ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
1
vote
7
replies
2.3k
views
Search all SRA data for sequence? Raw reads only
SRA
NCBI
Raw reads
fastq
updated 5 hours ago by
Wayne
★ 2.1k • written 4.3 years ago by
poppersrules
▴ 10
2
votes
2
replies
119
views
Forum:
Is this Rosalind inspired project actually useful?
python
code-review
6 hours ago by
Andrew
• 0
1
vote
1
reply
58
views
Subset a GAM (graph alignment) file
pangenome
vg
vgteam
updated 7 hours ago by
GenoMax
151k • written 7 hours ago by
Pau
• 0
0
votes
0
replies
51
views
News:
Reproducibility in Bioinformatics course
Conda
Singularity
Docker
Snakemake
Nextflow
7 hours ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
50
views
Any tips for optimizing an all vs all alignment with minimap2
mapping
nanopore
genomics
minimap2
8 hours ago by
Mark
▴ 50
0
votes
0
replies
53
views
Mismatch in orthology results from local alignment and phylogenetic analysis.
alignment
local
Phylogeny
global
updated 8 hours ago by
GenoMax
151k • written 8 hours ago by
Shakunthala Natarajan
• 0
2
votes
1
reply
96
views
How to automate blasting contigs?
assembly
contig
blast
WGS
updated 11 hours ago by
Mensur Dlakic
★ 29k • written 12 hours ago by
marongiu.luigi
▴ 740
0
votes
0
replies
59
views
Arecthere tools to find differences in biochemical pathways between organisms?
bioinformatics
biochemistry
pathways
differential
12 hours ago by
marongiu.luigi
▴ 740
0
votes
0
replies
55
views
DiffBind plot.profile error
DiffBind
BiocParallel
13 hours ago by
this_is_me_trying
• 0
1
vote
2
replies
122
views
Server Requirements for long read data analysis
longreadserver
longreadanalysis
serverrequirements
Server
updated 9 hours ago by
GenoMax
151k • written 13 hours ago by
genomics_student
• 0
0
votes
3
replies
673
views
News:
9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- FINAL CALL --
Workshop
RNA-Seq
transcriptomics
VariantCalling
DNA-Seq
13 hours ago by
ecSeq Bioinformatics
▴ 20
0
votes
3
replies
378
views
Random seed in scanpy
scanpy
scRNAseq
single-cell
updated 14 hours ago by
ATpoint
88k • written 6 days ago by
bioinfo
▴ 160
0
votes
1
reply
264
views
How to obtain the nodes in the graph corresponding to the variant in VCF
vg
updated 14 hours ago by
agis.maulana12
• 0 • written 5 days ago by
Wenhai
• 0
3
votes
4
replies
199
views
miRNA Quantifiaction Tool
quatification
mirna
updated 22 hours ago by
GenoMax
151k • written 1 day ago by
anthony.santana.703.j
▴ 30
0
votes
1
reply
141
views
WGCNA pickSoftThreshold problem
picksoftthreshold
question
problem
wgcna
updated 1 day ago by
LChart
4.9k • written 1 day ago by
ton_of_questions
• 0
2
votes
2
replies
434
views
plotProfile Errors of DiffBind
DiffBind
updated 1 day ago by
this_is_me_trying
• 0 • written 3 months ago by
lijiangres
▴ 20
7
votes
6
replies
273
views
Fungal Annotation Comparison
Annotation
RNAseq
Fungus
genome_assembly
funannotate
updated 1 day ago by
colindaven
7.5k • written 1 day ago by
SomeOne
▴ 180
0
votes
1
reply
211
views
Is comparing seeds sufficient, or should alignments be compared instead?
readmapping
updated 1 day ago by
shenwei356
8.7k • written 1 day ago by
curiousfellow@123
• 0
7
votes
2
replies
407
views
How to download protozoa reference genomes from NCBI
genomes
ncbi
updated 1 day ago by
colindaven
7.5k • written 7 days ago by
anna
▴ 70
2
votes
1
reply
213
views
Clustering on Big data (100 million samples)
Clustering
Data
Learning
Big
Machine
updated 1 day ago by
Mensur Dlakic
★ 29k • written 2 days ago by
Rushikesh
▴ 10
7
votes
7
replies
2.1k
views
6 follow
Where can I find a vcf file with individuals in it, that have a specific disease?
Phenotype
VCF
written 17 months ago by
Patrick
▴ 30
0
votes
2
replies
629
views
ERROR::INVALID_TAG_NM:Record A, Read name B, NM tag (nucleotide differences) in file [0] does not match reality [1]
bwa
1 day ago by
curious
▴ 890
5
votes
9
replies
669
views
Cut&Run TF Analysis - Very Low Peak Counts Despite Good Library Quality
macs2
cutandrun
chipseq
updated 7 days ago by
ATpoint
88k • written 7 days ago by
sk
▴ 20
0
votes
0
replies
136
views
Job:
Ensembl Genebuild Project Leader, EMBL-EBI, Hinxton near Cambridge, UK
Ensembl
jobs
updated 2 days ago by
GenoMax
151k • written 2 days ago by
A@Ensembl
▴ 30
0
votes
2
replies
189
views
tools to increase hi-c resolution
resolution
hi-c
1 day ago by
J.F.Jiang
▴ 930
2
votes
2
replies
212
views
How to fix this this tangle in my bacterial genome assembly
misassembly
assembly
genomics
ngs
14 hours ago by
Mark
▴ 50
5
votes
2
replies
373
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 2 days ago by
colindaven
7.5k • written 7 days ago by
biostars
▴ 30
0
votes
4
replies
261
views
Help configuring RepeatMasker
human
illumina
libraries
RepeatMasker
updated 2 days ago by
Michael
55k • written 2 days ago by
María José
▴ 10
0
votes
2
replies
189
views
How to process Iso-Seq files in SRA public fastqs
Iso-seq
19 hours ago by
Abieskawa
• 0
14
votes
19
replies
8.2k
views
10 follow
ACMG assignment tools
wes
acmg
WES
WGS
updated 2 days ago by
Prash
▴ 290 • written 5.0 years ago by
Eugene A
▴ 190
2
votes
0
replies
198
views
EggNOG-mapper problem
all
Hi
updated 2 days ago by
GenoMax
151k • written 3 days ago by
Salma
▴ 20
0
votes
0
replies
156
views
Colsep for dendrogram and ColSideColors in heatmap.2
Heatmap
DGE
EdgeR
heatmap.2
3 days ago by
fabian
▴ 10
1
vote
1
reply
232
views
Decision making on choosing the based on tblastn result
interpretation
tblastn
BLAST
E-score
updated 3 days ago by
GenoMax
151k • written 3 days ago by
srestha
• 0
9
votes
7
replies
3.0k
views
How to Identify the pathogenicity of a set of variants (by using ACMG guidelines)?
pathogenicity
SNP
variants
updated 4 days ago by
Damianos P. Melidis
▴ 60 • written 6.5 years ago by
DanielC
▴ 210
0
votes
4
replies
517
views
Why am I getting the exact same MarkDuplicates results when passing a query or coordinate sorted bam?
picard
bwa
updated 2 days ago by
GenoMax
151k • written 5 days ago by
curious
▴ 890
0
votes
2
replies
317
views
use AverageExpression to stratify samples
scRNA
2 days ago by
ndra1456
• 0
0
votes
0
replies
872
views
Multiple taxonomy hits per OTU ID in VSEARCH despite --top_hits_only (90% ID after QIIME2 clustering at 97%)
vsearch
updated 5 days ago by
GenoMax
151k • written 5 days ago by
salma.sarker
• 0
0
votes
0
replies
269
views
RepeatMasker output file question
RepeatMasker
5 days ago by
xinguok794
• 0
5
votes
1
reply
566
views
Which GWAS tool to use that can work on Czech cases and British controls, on a binary trait?
plink2
gwas
saige
updated 5 days ago by
LChart
4.9k • written 7 days ago by
anita.szabo08
▴ 10
1
vote
2
replies
382
views
Unsure whether or not I overcorrected for batch effect in dataset
Quality
Plot
PCA
Control
updated 5 days ago by
GenoMax
151k • written 5 days ago by
Megan
▴ 60
0
votes
3
replies
388
views
Primer removal in amplicon sequencing
removal
Primer
Amplicon
DADA2
sequencing
updated 5 days ago by
GenoMax
151k • written 5 days ago by
sxf520
• 0
0
votes
1
reply
386
views
GATK BQSR error — Reference and BAM file chromosome name mismatch (“chr” vs. no “chr”)
GATK
VCF
BSQR
updated 5 days ago by
Ram
45k • written 6 days ago by
iamsmor
• 0
0
votes
1
reply
333
views
Batch correction without biological covariates
Combat-seq
RNA-seq
batch-correction
updated 5 days ago by
Ram
45k • written 6 days ago by
as823jk
• 0
2
votes
3
replies
393
views
RagTag results
NGS
scaffolding
RagTag
gaps
updated 6 days ago by
shelkmike
★ 1.6k • written 6 days ago by
synthiiihuh
• 0
121,301 results • Page
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Answer: How to interpret two letter codes of COG category obtained from EggNOG tool?
MACS2 with multiple replicates
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Answer: Subset a GAM (graph alignment) file
Answer: Is this Rosalind inspired project actually useful?
Answer: Is this Rosalind inspired project actually useful?
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Recent Replies
Answer: GSEA analysis in R
by
ATpoint
88k
It doesn't matter really. Both shrunken logFCs and test statistics are fine and there is no real justification of one over the other. This …
Comment: ATAC-seq analysis
by
GenoMax
151k
Name sorting would be essential only if you were converting a BAM to fastq reads or marking duplicates. To visualize the data position sort.
Comment: Assembly issues
by
GenoMax
151k
Please post `galaxy` related help questions on their help forum for prompt response: https://help.galaxyproject.org/ They can see your dat…
Comment: Use taxdb tp get scientific names in local BLAST output
by
GenoMax
151k
> Do I need to get the taxids in a different way in this case? Yes. You can get the accession to taxID mapping file from https://ftp.ncbi.…
Comment: is there a way to get SRA info (Paired Library, Sample id, Seq Tech... etc) usin
by
Wayne
★ 2.1k
Tagging this with a comment because the expansive title of the original question makes this feature prominently in search results... Ther…
Comment: Use taxdb tp get scientific names in local BLAST output
by
Luca Arbore
▴ 10
Thank you very much Genomax. Now, because there may be a misunderstanding I need to clarify the following: I do not have the nt database d…
Answer: Search all SRA data for sequence? Raw reads only
by
Wayne
★ 2.1k
There's now [Logan Search](https://logan-search.org/). (presently it covers through the end of 2023) >"Given a DNA sequence, the service…
Comment: Is this Rosalind inspired project actually useful?
by
Andrew
• 0
Thanks for the reply! It definitely has been useful on a personal level to grow the functionality of this for my specific use case because…
Answer: Is this Rosalind inspired project actually useful?
by
jared.andrews07
★ 18k
That functionality can be found in [biopython](https://biopython.org/wiki/Documentation), which is the most general bioinformatics toolkit …
Answer: Subset a GAM (graph alignment) file
by
glenn.hickey
▴ 530
For the first 1000 reads: ``` vg view -a myreads.gam | head -n1000 | vg view -a -G -J - > myreads_1000.gam ``` For downsampling like …
Answer: Use taxdb tp get scientific names in local BLAST output
by
GenoMax
151k
With `blast+ v.2.16`. Get the sequences for `diptera` from "nt" blast db. $ blastdbcmd -db nt -taxids 7147 -outfmt %f > test.fa Whil…
Comment: Still bad phred score after fastp
by
Arup Ghosh
3.3k
By default, the quality score threshold is `15`. So if you have not specified a value for `--qualified_quality_phred` or `--average_qual`, …
Comment: Server Requirements for long read data analysis
by
GenoMax
151k
EPI2ME workflows available from ONT for sake of completeness: https://nanoporetech.com/products/analyse/epi2me A number of pre-made NF wor…
Answer: How to automate blasting contigs?
by
Mensur Dlakic
★ 29k
There is nothing to automate if all the contigs are in a single file. blastn -query contigs.fna -db nr -task blastn -out contigs_vs_nr…
Comment: Use taxdb tp get scientific names in local BLAST output
by
Luca Arbore
▴ 10
Thank you for replies. Fast headers of downloaded sequences look like this grep "^>" diptera_coi_030625.fasta | head -n 5 >AB0…
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