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26 results • Page
1 of 1
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Votes
Replies
0
votes
1
reply
24
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 1 hour ago by
GenoMax
141k • written 1 hour ago by
Srinka
▴ 20
0
votes
1
reply
25
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
updated 1 hour ago by
GenoMax
141k • written 1 hour ago by
njornet
▴ 20
0
votes
0
replies
15
views
Software to calculate RSCU, ENC other than codonw
rscu
bioinformatics
codonw
2 hours ago by
SHREYA
• 0
0
votes
0
replies
21
views
Merging replicates from Encode project
CHIP-seq
encode
2 hours ago by
Nurken
• 0
1
vote
3
replies
114
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
3 hours ago by
WouterDeCoster
47k
0
votes
2
replies
71
views
some error in building kraken2 database
metagenome
database
bioinformatics
kraken2
updated 2 hours ago by
GenoMax
141k • written 4 hours ago by
Art1ess
• 0
0
votes
0
replies
29
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
4 hours ago by
Susmita Mandal
▴ 110
0
votes
1
reply
69
views
Failed kmer content
content
kmer
illumina
ngs
updated 2 hours ago by
GenoMax
141k • written 7 hours ago by
Kasturi
• 0
0
votes
1
reply
92
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 6 hours ago by
Basti
★ 2.0k • written 8 hours ago by
qudrat.nii
▴ 10
0
votes
0
replies
52
views
Seurat merge and batch correction
Seurat
10 hours ago by
sooni
▴ 20
0
votes
0
replies
38
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
R
Copy-number-analysis
gc.wig
genome
10 hours ago by
SSSJec
• 0
0
votes
1
reply
96
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 18 hours ago by
Ram
43k • written 18 hours ago by
Cameron.walker9900
• 0
0
votes
8
replies
227
views
Error in cnetplot enrichplot package
R
updated 17 hours ago by
Ram
43k • written 19 hours ago by
Farhad
• 0
0
votes
0
replies
71
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 19 hours ago by
Ram
43k • written 19 hours ago by
maxime.policarpo
▴ 200
0
votes
0
replies
58
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 19 hours ago by
Ram
43k • written 19 hours ago by
sansan_96
▴ 80
0
votes
2
replies
116
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
17 hours ago by
dxj294
• 0
0
votes
0
replies
61
views
File with NCBI summary or Uniprot description
annotation
function
visualisation
bulk
NCBI
Uniprot
RNA
3 hours ago by
Amélie
• 0
0
votes
0
replies
92
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 19 hours ago by
Ram
43k • written 20 hours ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 17 hours ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
0
votes
0
replies
67
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 21 hours ago by
GenoMax
141k • written 22 hours ago by
Abeer
• 0
0
votes
1
reply
107
views
tbtool
tbtool
updated 22 hours ago by
Ram
43k • written 22 hours ago by
Raman
• 0
0
votes
2
replies
157
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 20 hours ago by
i.sudbery
19k • written 23 hours ago by
Patadu94
• 0
0
votes
2
replies
130
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 19 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
emmanouil.a
▴ 120
0
votes
0
replies
63
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
3 hours ago by
alifafiq1
• 0
2
votes
3
replies
165
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
updated 4 hours ago by
Pierre Lindenbaum
161k • written 1 day ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
271
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 19 hours ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
26 results • Page
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Recent Votes
The Biostar Herald for Monday, April 15, 2024
The Biostar Herald for Monday, April 15, 2024
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
Answer: Gene set enrichment analysis differences between 2020 and 2024
Answer: Fast way to extract specific sequences from large fasta
Answer: Fast way to extract specific sequences from large fasta
Comment: Intersect multiple BED files
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Recent Awards •
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Scholar
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anovak
▴ 110
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pfee418
▴ 10
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sarahmanderni
▴ 100
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54k
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Recent Replies
Comment: Using vg gamsort with naive sorting algorithm
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
The scope is all publications related to grants from an NIH award program. There are currently ~120k publications in total (about a few hun…
Answer: Using vg gamsort with naive sorting algorithm
by
anovak
▴ 110
The `-d` sorting mode does the entire sort in memory, so it will only work if you have enough memory to load your whole GAM file. To fin…
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
I have a list of PMIDs for publications linked to a list of grants, exported from NIH RePORTER.
Comment: Plot DNA methylation level of DMR on the basis of certain genes
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Should I remove unlocalized scaffols in reference genome before alignment?
by
GenoMax
141k
Yes you can remove those if you are only interested in annotated genes.
Comment: Help for coding: Trinity for differential gene expression studies
by
mchour
• 0
[This could help][1] [1]: https://github.com/trinityrnaseq/RNASeq_Trinity_Tuxedo_Workshop/wiki/Trinity-De-novo-Transcriptome-Assembly-W…
Answer: How to compare the quality of assemblies
by
colindaven
6.4k
Are you sure you have looked into the HiFiasm output files (fasta and GFA) in detail and excluded non-primary contigs, hap1, hap2 and other…
Answer: How to identify gaps in a genome?
by
colindaven
6.4k
You can use seqtk to find gaps in a fasta https://github.com/lh3/seqtk seqtk gap Usage: seqtk gap [-l 50] <in.fa>
Comment: some error in building kraken2 database
by
GenoMax
141k
> Obviously, running kraken2 after the build is complete does not produce the correct results What do you get instead? Error/no output? Ha…
Comment: Failed kmer content
by
GenoMax
141k
Can you post a screenshot of what you are referring to? Why did you choose to "clean" your data? FastQC analysis needs to be done keeping…
Comment: Help for coding: Trinity for differential gene expression studies
by
rhossen
• 0
It should be great if I have any assistance in my build up command using trinity package...
Comment: Filter BAM to keep only alignments at an interval, ignoring reads spliced over
by
WouterDeCoster
47k
I want reads in a specific short interval, but if I do that with samtools view I also get reads that are spliced over that interval.
Answer: Help for coding: Trinity for differential gene expression studies
by
mchour
• 0
Hello, I would recommend following RSEM wiki for more information about the options, or even run RSEM directly, not with the script provi…
Answer: WGCNA preservation analysis
by
Michael
54k
This seems like a model case for why we need better sustainable bioinformatics data and services. I don't know the exact background behind …
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