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129 results • Page 2 of 3
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0
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0
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134
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How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 2 days ago by 43k • written 3 days ago by • 0
0
votes
0
replies
136
views
Bacterial genome alignment with mauve
Bacteria mauve genome
3 days ago by rthapa ▴ 90
0
votes
0
replies
128
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Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
3 days ago by Mamatha Y S • 0
0
votes
2
replies
245
views
bam merging for archaic samples
samtools bam
updated 2 days ago by 43k • written 3 days ago by ▴ 100
1
vote
0
replies
534
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
4 days ago by mathavanbioinfo ▴ 90
0
votes
0
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205
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Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
3 days ago by abhishekghadge • 0
2
votes
5
replies
669
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 3 days ago by ▴ 740 • written 4 days ago by ★ 2.4k
0
votes
0
replies
182
views
agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 4 days ago by 43k • written 4 days ago by • 0
0
votes
0
replies
185
views
scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
4 days ago by Nitin • 0
0
votes
0
replies
185
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by 43k • written 4 days ago by ▴ 60
0
votes
0
replies
178
views
Chemical structure validation
structure cap validation metabolite
4 days ago by Rodolfo Adrián • 0
0
votes
1
reply
255
views
Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 4 days ago by 141k • written 4 days ago by ▴ 10
0
votes
0
replies
200
views
Copy number variation plot
Copy-number-variation genomics
updated 4 days ago by 43k • written 4 days ago by • 0
0
votes
0
replies
173
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
4 days ago by DanielEB_fisk ▴ 20
0
votes
1
reply
277
views
Could you please assist in identifying this cluster?
single-cell
updated 4 days ago by 43k • written 4 days ago by • 0
0
votes
0
replies
192
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 4 days ago by 43k • written 5 days ago by • 0
0
votes
0
replies
190
views
miRDeep2: How to get the read counts
mirdeep2
5 days ago by Atul K. • 0
0
votes
0
replies
198
views
Lncipedia GTF file error
Proteomics
updated 4 days ago by 43k • written 5 days ago by ▴ 10
3
votes
3
replies
459
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 4 days ago by 14k • written 5 days ago by ▴ 510
0
votes
2
replies
529
views
How to get the reference panel for UKBB
UKBB GWAS clump
5 days ago by 航太郎 • 0
0
votes
0
replies
208
views
create genewise sync file in popoolation
popoolation
updated 5 days ago by 141k • written 5 days ago by • 0
0
votes
2
replies
366
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
5 days ago by Ashok • 0
0
votes
2
replies
406
views
miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
5 days ago by Ashok • 0
0
votes
0
replies
207
views
Variant Generation Using Longshot
long-reads variant-calling ONT minion longshot
updated 5 days ago by 43k • written 5 days ago by ▴ 10
0
votes
2
replies
414
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
4 days ago by _quantum_girl_ ▴ 10
0
votes
0
replies
197
views
traying to make a maf from an already annotated vcf
vcf vcf2maf maf maftools VEP
1 day ago by Javier • 0
0
votes
0
replies
172
views
Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
5 days ago by enferdeflame • 0
1
vote
1
reply
405
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
updated 3 days ago by ★ 7.0k • written 5 days ago by ▴ 260
0
votes
1
reply
397
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 5 days ago by 43k • written 19 months ago by • 0
0
votes
0
replies
155
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score tspex
updated 5 days ago by 43k • written 6 days ago by ▴ 10
0
votes
0
replies
171
views
How to root an unrooted tree with a known root tree?
phylogenetics rooting R
6 days ago by P. • 0
0
votes
0
replies
163
views
Issues with SnpEff Assuming Circular Chromosomes in Eukaryotic Genome Analysis
snpEff
6 days ago by ekirsch • 0
1
vote
1
reply
379
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
4 days ago by renan.igor • 0
0
votes
0
replies
169
views
filter the most significant ligand and receptors in netVisual_bubble in cell chat
cellchat
6 days ago by synat.keam ▴ 100
0
votes
1
reply
261
views
assembly using CCS, CLR, CCS_CLR sequences together?
assembly
updated 6 days ago by 141k • written 6 days ago by • 0
0
votes
4
replies
571
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
5 days ago by Kai Xin • 0
1
vote
1
reply
219
views
Retrieve a % coverage for each transcript
RNA-seq
updated 6 days ago by 43k • written 6 days ago by ▴ 40
0
votes
2
replies
362
views
How can I solve this error?
metal
6 days ago by 22211020193 • 0
0
votes
0
replies
162
views
Struggling to lift genome builds
PLINK liftover GWAS
updated 6 days ago by 141k • written 6 days ago by • 0
1
vote
2
replies
267
views
Can I readmap short reads to rDNA references?
rDNA assembly
updated 6 days ago by 43k • written 6 days ago by • 0
0
votes
0
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350
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer ATAC-seq
6 days ago by Ronin • 0
2
votes
7
replies
800
views
Removing duplicates
duplicates ONT minimap2
updated 5 days ago by ▴ 510 • written 7 days ago by • 0
0
votes
1
reply
180
views
Freyja plot error
Freyja
updated 6 days ago by 43k • written 7 days ago by • 0
0
votes
4
replies
489
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx deconcolution
6 days ago by feather-W • 0
0
votes
2
replies
306
views
GSEA analysis in R
GSEA R Arabidopsis
6 days ago by Sudip • 0
1
vote
2
replies
223
views
permutation test in edgeR
rna-seq edgeR
updated 2 days ago by ★ 7.0k • written 16 days ago by • 0
0
votes
6
replies
401
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 2 hours ago by • 0 • written 22 days ago by ▴ 20
0
votes
2
replies
534
views
autodockvina
python python3 autodock
updated 5 days ago by 43k • written 3 months ago by • 0
0
votes
0
replies
272
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness IBD GWAS
updated 1 day ago by 43k • written 14 months ago by ▴ 10
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 5 days ago by 43k • written 18 months ago by • 0
129 results • Page 2 of 3
Recent Votes
Answer: To get p-values for the TPM
Comment: To get p-values for the TPM
A: Finding the centromere and telomere of cattle genome (Bos Taurus)
A: How to systematically check if a bam file is truncated
Comment: some error in building kraken2 database
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
C: RSeQC Output from infer_experiment.py - what does it mean?
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Recent Replies
Comment: different FeatureCounts output for the same data by GenoMax 141k
> featureCounts alignment rate is only around 15-20%. You mean assignment rate? It is that low even after allowing for counting of multi-m…
Comment: alignment result by GenoMax 141k
> 20386810 (88.67%) aligned concordantly exactly 1 time This result is fine.
Comment: To get p-values for the TPM by ATpoint 82k
Seconding that. Just use established pipelines, tximport => DESeq2, get your stats and call it a day. Custom pipelines paired with little e…
Comment: Should I remove unlocalized scaffols in reference genome before alignment? by njornet ▴ 20
I don't want reads incorrectly aligned to these scaffolds and loose information of relevant regions, but as you said that probably won't ha…
Comment: To get p-values for the TPM by dsull ★ 5.8k
Your post should be a "com, not an "answer". Use "Add Comment" to request clarifications on an answer someone has provided. tximport can t…
Comment: Use of Kraken output for functional analysis by gv • 0
Hello, you can use kraken-biom [kraken_biom.py] tool to get your Biom file from input kreport cheers,
Comment: To get p-values for the TPM by VITALA • 0
sir, deseq2 takes counts as inputs rightfor the hypothesis testing /to see the variance between the two groups, but in my case what i want …
Answer: To get p-values for the TPM by dsull ★ 5.8k
There are plenty of RSEM -> tximport -> DESeq2 tutorials online. Just follow one of those. DESeq2 will give you "p values" based on a Wa…
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by dsull ★ 5.8k
I agree for the most part. However, Heng Li has argued that the one application that they are essential for is short read variant calling. …
Comment: interpretartion of a vcf file by samuelkalandarov2002 ▴ 10
In my case , there is only one sample : here is an example of a some variants generated using minipileup : #CHROM POS ID REF ALT QUAL FI…
Comment: How to calculate identity percentage between proteins contained in a FASTA file? by b.contreras.moreira ▴ 170
This should work if you know your sequences are related and can be globally aligned; otherwise it is safer to compute local alignments (for…
Comment: How to compare the quality of assemblies by kirillkirilenko ▴ 40
A haploid assembly is our goal. For purging we used prefix.p_ctg.gfa (assembly graph of primary contigs).
Comment: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File? by Istvan Albert 100k
What I mean is that no sequencing run can be calibrated with the claimed precision. Where it could correctly distinguish between basecalls …
Comment: HaplotypeCaller - only SNPs by analyst ▴ 20
After HaplotypeCaller, you can use gatk SelectVariants to extract snps or indels from vcf file ([link to command][1]) [1]: https://gatk…
Comment: GTF file for Rhinolophus sinicus by atowns21 • 0
Ah gotcha. I guess what doesn't make sense to me is why a [paper][1] published in 2022 uses that reference genome. [1]: https://www.na…
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