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105 results • Page 2 of 3
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124
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CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 3 days ago by 8.7k • written 3 days ago by • 0
2
votes
5
replies
429
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Marking duplicates using UMIs
Deduplication UMI
updated 3 days ago by 19k • written 4 days ago by • 0
0
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0
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136
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How to extract the mutations specific to cancer after variant annotation
variant-annotation
updated 3 days ago by 43k • written 4 days ago by • 0
0
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0
replies
138
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Bacterial genome alignment with mauve
Bacteria mauve genome
4 days ago by rthapa ▴ 90
0
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0
replies
131
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Reparametrization of .str (param penalty > 100) File from CGenFF for Ligand Simulation in GROMACS
Simulation CGenFF Gromacs VMD
4 days ago by Mamatha Y S • 0
0
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2
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256
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bam merging for archaic samples
samtools bam
updated 3 days ago by 43k • written 4 days ago by ▴ 100
1
vote
0
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537
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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
5 days ago by mathavanbioinfo ▴ 90
0
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0
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209
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Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
4 days ago by abhishekghadge • 0
2
votes
5
replies
676
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 4 days ago by ▴ 740 • written 5 days ago by ★ 2.4k
0
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0
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185
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agilent microarray gpl data does not have gene symbol column
microarray agilent gpl
updated 5 days ago by 43k • written 5 days ago by • 0
0
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0
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186
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scRNA Cluster frequency
CV PCA scRNA Cluster-Frequency
5 days ago by Nitin • 0
0
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0
replies
186
views
absolute path for symbolic links in Snakefile
Snakemake
updated 5 days ago by 43k • written 5 days ago by ▴ 60
0
votes
0
replies
179
views
Chemical structure validation
structure cap validation metabolite
5 days ago by Rodolfo Adrián • 0
0
votes
1
reply
259
views
Downloading the raw microarray data from GEO
.gpr microarray .CEL
updated 5 days ago by 141k • written 5 days ago by ▴ 10
0
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0
replies
202
views
Copy number variation plot
Copy-number-variation genomics
updated 5 days ago by 43k • written 5 days ago by • 0
0
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0
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175
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SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs ngsTools ANGSD genomics
5 days ago by DanielEB_fisk ▴ 20
0
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1
reply
279
views
Could you please assist in identifying this cluster?
single-cell
updated 5 days ago by 43k • written 5 days ago by • 0
0
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0
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193
views
Conversion to tree format
PLINK bed Figtree SplitsTree
updated 5 days ago by 43k • written 5 days ago by • 0
0
votes
0
replies
192
views
miRDeep2: How to get the read counts
mirdeep2
6 days ago by Atul K. • 0
0
votes
0
replies
199
views
Lncipedia GTF file error
Proteomics
updated 5 days ago by 43k • written 6 days ago by ▴ 10
3
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3
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462
views
Free/open source 23andme-like analysis
SNPs genomics NGS VCF
updated 5 days ago by 14k • written 6 days ago by ▴ 510
0
votes
2
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532
views
How to get the reference panel for UKBB
UKBB GWAS clump
6 days ago by 航太郎 • 0
0
votes
0
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213
views
create genewise sync file in popoolation
popoolation
updated 6 days ago by 141k • written 6 days ago by • 0
0
votes
2
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372
views
error in coding potential calculator CPC2
cpc CPC2 coding-potential
6 days ago by Ashok • 0
0
votes
2
replies
410
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miRNAs quantification using mirdeep2 tool
differential-expression mirdeep2 miRNA
6 days ago by Ashok • 0
0
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0
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210
views
Variant Generation Using Longshot
long-reads variant-calling ONT minion longshot
updated 6 days ago by 43k • written 6 days ago by ▴ 10
0
votes
2
replies
417
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control SNV QC SNP
5 days ago by _quantum_girl_ ▴ 10
0
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0
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200
views
traying to make a maf from an already annotated vcf
vcf vcf2maf maf maftools VEP
2 days ago by Javier • 0
0
votes
0
replies
175
views
Pruning with plink finds a majority of SNPs in very high LD
LD SNP plink pruning
6 days ago by enferdeflame • 0
1
vote
1
reply
411
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA Limma
updated 4 days ago by ★ 7.0k • written 6 days ago by ▴ 260
0
votes
1
reply
398
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 6 days ago by 43k • written 19 months ago by • 0
0
votes
0
replies
157
views
How can I obtain the tissue or sample name alongside the Tau score in tspex?
tau-score tspex
updated 6 days ago by 43k • written 7 days ago by ▴ 10
1
vote
1
reply
388
views
Load a full GFF3 into annotation track using arrow (Apollo)
arrow python-apollo Apollo
5 days ago by renan.igor • 0
0
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4
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572
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
6 days ago by Kai Xin • 0
2
votes
7
replies
805
views
Removing duplicates
duplicates ONT minimap2
updated 6 days ago by ▴ 510 • written 7 days ago by • 0
1
vote
2
replies
226
views
permutation test in edgeR
rna-seq edgeR
updated 3 days ago by ★ 7.0k • written 17 days ago by • 0
0
votes
6
replies
423
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 1 day ago by • 0 • written 23 days ago by ▴ 20
0
votes
2
replies
537
views
autodockvina
python python3 autodock
updated 6 days ago by 43k • written 4 months ago by • 0
0
votes
0
replies
273
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness IBD GWAS
updated 2 days 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 6 days ago by 43k • written 18 months ago by • 0
0
votes
0
replies
730
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq scRNA-Seq batch-effect
updated 6 days ago by 43k • written 3.4 years ago by ▴ 180
0
votes
1
reply
818
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR Batch-effect RNA-Seq
updated 6 days ago by 43k • written 3.7 years ago by • 0
0
votes
0
replies
1.2k
views
Batch estimate using kBET
batch-effect kbet
updated 6 days ago by 43k • written 4.0 years ago by • 0
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell Batch-effect RNA-Seq Scran
updated 6 days ago by 43k • written 5.5 years ago by ▴ 10
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 4 days ago by • 0 • written 6.5 years ago by ▴ 30
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS exome-sequencing batch-effect
updated 6 days ago by 43k • written 6.5 years ago by ▴ 270
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq batch-effect
updated 6 days ago by 43k • written 6.6 years ago by ▴ 80
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq batch-effect sequencing
updated 6 days ago by 43k • written 6.9 years ago by • 0
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect RNA-Seq ARSyNseq limma NOISeq
updated 6 days ago by 43k • written 6.9 years ago by • 0
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 6 days ago by 43k • written 7.1 years ago by ▴ 310
105 results • Page 2 of 3
Recent Votes
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
A: What is the VEP Impact column?
is oxford nanopore technology data paired or single end sequencing?
is oxford nanopore technology data paired or single end sequencing?
Answer: is oxford nanopore technology data paired or single end sequencing?
Answer: Trying to wrap my head around Illumina paired end sequencing
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Answer: Finding orthologs between genome error by Adrian Altenhoff ★ 1.1k
Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
Comment: Fetch table from clinvar database according to a list of rsid by ashaneev07 ▴ 20
so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
Comment: To get p-values for the TPM by dsull ★ 5.8k
OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid 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: different FeatureCounts output for the same data by sehriban.buyukkilic ▴ 10
Sure, I'll inquire about the version of Rsubread. I'll keep you posted if it works :) Thanks
Comment: different FeatureCounts output for the same data by sehriban.buyukkilic ▴ 10
Yeah, let me show you my featureCounts result, it looks like this. It's too low. [1]: /media/images/eb8293fe-e6ae-4b02-92e2-0ba2075b
Comment: Adding CB tag to bam file by Pierre Lindenbaum 161k
samtools addreplacerg is for read groups. This is not what OP asked.
Comment: Adding CB tag to bam file by Maria • 0
When I try ``` samtools addreplacerg -r "@CB\tID:$cell" -o $cell.bam $LINE``` the CB tag gets add to the header, but the tag in every line …
Answer: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid by Pierre Lindenbaum 161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid by Pierre Lindenbaum 161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data by ATpoint 82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by Bertalan_Takacs ▴ 90
Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in by b.contreras.moreira ▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM by VITALA • 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
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