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521 results • Page 1 of 11
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0
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2
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73
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bam merging for archaic samples
samtools bam ancient merge
3 hours ago by Matteo Ungaro ▴ 100
1
vote
0
replies
175
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers TRINITY
9 hours ago by mathavanbioinfo ▴ 90
0
votes
0
replies
118
views
Using samtools with GCS (google cloud storage) on docker a docker container seems to give "Protocol Not Supported" error
samtools gcs
19 hours ago by abhishekghadge • 0
0
votes
3
replies
319
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq gene-expression
updated 13 hours ago by 43k • written 19 hours ago by ▴ 140
1
vote
4
replies
417
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 19 hours ago by 4.5k • written 21 hours ago by ★ 2.4k
0
votes
0
replies
105
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 20 hours ago by 43k • written 22 hours ago by • 0
0
votes
0
replies
110
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
22 hours ago by Nitin • 0
0
votes
0
replies
114
views
absolute path for symbolic links in Snakefile
Snakemake
updated 22 hours ago by 43k • written 22 hours ago by ▴ 60
0
votes
0
replies
105
views
Chemical structure validation
structure cap validation metabolite
23 hours ago by Rodolfo Adrián • 0
0
votes
1
reply
177
views
Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 23 hours ago by 141k • written 23 hours ago by ▴ 10
0
votes
0
replies
123
views
Copy number variation plot
Copy-number-variation genomics
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
0
replies
106
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
1 day ago by DanielEB_fisk ▴ 20
0
votes
1
reply
204
views
Could you please assist in identifying this cluster?
single-cell
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
0
replies
127
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 1 day ago by 43k • written 1 day ago by • 0
0
votes
0
replies
128
views
miRDeep2: How to get the read counts
mirdeep2
1 day ago by Atul K. • 0
0
votes
0
replies
134
views
Lncipedia GTF file error
Proteomics
updated 1 day ago by 43k • written 1 day ago by ▴ 10
3
votes
3
replies
360
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 8 hours ago by 14k • written 1 day ago by ▴ 510
0
votes
2
replies
442
views
How to get the reference panel for UKBB
UKBB GWAS clump
1 day ago by 航太郎 • 0
0
votes
0
replies
147
views
create genewise sync file in popoolation
popoolation
updated 1 day ago by 141k • written 1 day ago by • 0
0
votes
2
replies
307
views
python file for coding potential calculator
cpc2.py
1 day ago by Ashok • 0
0
votes
2
replies
297
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
1 day ago by Ashok • 0
0
votes
2
replies
333
views
miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
1 day ago by Ashok • 0
0
votes
0
replies
152
views
Variant Generation Using Longshot
long-reads variant-calling ONT minion longshot
updated 2 days ago by 43k • written 2 days ago by • 0
0
votes
2
replies
352
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
1 day ago by _quantum_girl_ ▴ 10
0
votes
0
replies
159
views
traying to make a maf from an already annotated vcf
vcf2maf VEP maftools
updated 2 days ago by 43k • written 2 days ago by • 0
0
votes
0
replies
153
views
Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
2 days ago by enferdeflame • 0
0
votes
0
replies
166
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
1 day ago by Chris ▴ 260
0
votes
1
reply
393
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 2 days ago by 43k • written 19 months ago by • 0
0
votes
0
replies
147
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score tspex
updated 2 days ago by 43k • written 2 days ago by ▴ 10
0
votes
0
replies
160
views
How to root an unrooted tree with a known root tree?
phylogenetics rooting R
2 days ago by P. • 0
0
votes
0
replies
154
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
2 days ago by ekirsch • 0
1
vote
1
reply
340
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
23 hours ago by renan.igor • 0
0
votes
0
replies
152
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
2 days ago by synat.keam ▴ 100
0
votes
1
reply
242
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 2 days ago by 141k • written 2 days ago by • 0
0
votes
4
replies
544
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
1 day ago by Kai Xin • 0
1
vote
1
reply
208
views
Retrieve a % coverage for each transcript
RNA-seq
updated 2 days ago by 43k • written 2 days ago by ▴ 40
0
votes
2
replies
336
views
How can I solve this error?
metal
2 days ago by 22211020193 • 0
0
votes
0
replies
157
views
Struggling to lift genome builds
PLINK liftover GWAS
updated 2 days ago by 141k • written 3 days ago by • 0
1
vote
2
replies
245
views
Can I readmap short reads to rDNA references?
rDNA assembly
updated 2 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
310
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer ATAC-seq
3 days ago by Ronin • 0
2
votes
7
replies
744
views
Removing duplicates
duplicates ONT minimap2
updated 1 day ago by ▴ 510 • written 3 days ago by • 0
0
votes
1
reply
176
views
Annotating a dataset with gnomAD v4 using Hail
Python Sequencing Hail Exome Annotation
updated 3 days ago by ▴ 40 • written 3 days ago by • 0
0
votes
1
reply
165
views
Freyja plot error
Freyja
updated 3 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
143
views
BIOM format can contain tabular data ?
BIOM phyloseq biomformat R
3 days ago by chemokine-1 ▴ 10
0
votes
4
replies
454
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx deconcolution
2 days ago by feather-W • 0
0
votes
2
replies
190
views
Bedmethyl file format
bedmethyl methylation
updated 3 days ago by 141k • written 3 days ago by ▴ 20
0
votes
0
replies
158
views
sequence table for DADA2 chimera filtering
OTU sequencetable DADA2
3 days ago by Ali • 0
2
votes
4
replies
285
views
SnpEff annotates coding duplication as intronic?
snpeff
3 days ago by kirill.zaslavsky • 0
0
votes
2
replies
220
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics scRNA-seq proliferation
3 days ago by mropri ▴ 150
0
votes
0
replies
133
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames RNA-Seq WGCNA unique
3 days ago by shasabhi1 • 0
521 results • Page 1 of 11
Recent Votes
Answer: MEGA Analysis Issue on High-Performance Computer
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
Answer: Ubuntu storage space is decreasing automatically
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Answer: Cellranger count error: Input FASTQ file ended prematurely
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Comment: MEGA Analysis Issue on High-Performance Computer by 5heikki 11k
16GB of RAM is nothing. My phone has that. My server has 1TB of RAM, and even that isn't always enough
Comment: MEGA Analysis Issue on High-Performance Computer by GenoMax 141k
I don't think MEGA supports GPU's: https://www.megasoftware.net/web_help_11/Part_I_Getting_Started/Installing_MEGA/System_Requirements.htm
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by ATpoint 81k
You can, if you use RStudio via Docker, for example `bioconductor/bioconductor_docker`. I currently manage many different projects with thi…
Comment: bam merging for archaic samples by Matteo Ungaro ▴ 100
@Pierre Lindenbaum I see. So, I can actually manipulate just one single RG tag at the time with `samtools`? Which flag should I use, or sho…
Comment: bam merging for archaic samples by Pierre Lindenbaum 161k
RG tag "L9302" is missing the the BAM header. You should have something like this in the BAM header ``` @RG ID:L9302 SM:L9302 ``` may be…
Answer: Filtering sam or bam file with maximum matching region by Pierre Lindenbaum 161k
> . Is there any way to find through sam or bam file that which chromosomal position are maximum reads aligning to? samtools depth i…
Comment: Calculate Radius of Gyration [python 3] by ndm1096 • 0
Hello Franco. I am very much new with bioinformatics but I have been tasked with studying the radius of gyration of a timeseries of a prote…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach by BioinfGuru ★ 1.7k
That makes a lot more sense. Thank you.
Answer: Removing Illumina microarray probes with no expression HumanHT-12v4 by Gordon Smyth ★ 7.0k
Type ``` help("read.idat") ``` and read the example at the bottom of the page, which shows you how to set the `other$Detection` component o…
Comment: Free/open source 23andme-like analysis by swbarnes2 14k
Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really…
Comment: Cellranger count error: Input FASTQ file ended prematurely by swbarnes2 14k
If _1 and _2 really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but dif…
Comment: Cellranger count error: Input FASTQ file ended prematurely by ATpoint 81k
Just delete the index read files. They just take up space and will never be used.
Comment: Adding CB tag to bam file by swbarnes2 14k
Yes. Why wouldn't you use, say, AddOrReplaceReadsGroups?
Comment: Ciriquant not configuring hisat2 indexed files by Atul K. • 0
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2 by Ram 43k
See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
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