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121,984 results • Page 252 of 2440
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2
votes
4
replies
1.1k
views
Filter VCF file for variant alleles
VCF bcftools vcftools
updated 2.3 years ago by 45k • written 2.4 years ago by ▴ 20
2
votes
4
replies
2.6k
views
PacBio Pipeline and Tools for Variant Call
longread pacbio whatshap pbmm2
2.4 years ago by Kiran ▴ 80
0
votes
0
replies
594
views
Count hexamer bias from pair end short read data
short DESeq2 bias read hexamer
updated 2.4 years ago by 13k • written 2.4 years ago by ▴ 60
1
vote
0
replies
490
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
2.4 years ago by fr ▴ 220
3
votes
3
replies
1.3k
views
Can any one suggest tools that generate "mind-maps" on concepts in biology/biotech?
Mind-maps
updated 2.4 years ago by 4.8k • written 2.4 years ago by • 0
3
votes
2
replies
873
views
Panther db Reference List
pantherdb enrichment-tests
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 260
0
votes
1
reply
878
views
ABO alleles
ABO variants SNPs alleles
updated 2.4 years ago by ★ 1.5k • written 2.4 years ago by • 0
1
vote
1
reply
1.2k
views
How to determine the exact version of hg38 if I have only the FASTA file
reference-genome FASTA
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
0
votes
2
replies
1.2k
views
readGenericHeader() error message Limma
rna limma microarray genomics normalization
2.4 years ago by survive • 0
1
vote
1
reply
726
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial PacBio SRA Mitogenome
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 40
2
votes
1
reply
1.2k
views
sctransform on scRNA seq
seurat
updated 2.4 years ago by 89k • written 2.4 years ago by ▴ 30
1
vote
4
replies
3.1k
views
Dot Plot using KEGG
KEGG DotPlot GO
2.4 years ago by smanzano250800 • 0
13
votes
25
replies
6.4k
views
7 follow
VEP output has no gene names
alignment sequencing vep
updated 2.4 years ago by ★ 2.5k • written 7.2 years ago by ▴ 240
11
votes
23
replies
3.4k
views
gatk Hardfilter Error
hardfilter
updated 2.4 years ago by 56k • written 2.4 years ago by ▴ 30
3
votes
3
replies
1.4k
views
WGCNA: many over and under-expressed features in modules of a signed network
WGCNA
updated 2.4 years ago by 3.9k • written 2.4 years ago by ▴ 350
1
vote
7
replies
3.1k
views
Docker Error while running nf-core/rnaseq pipeline
RNA-seq nf-core docker
updated 2.4 years ago by 89k • written 2.4 years ago by • 0
2
votes
3
replies
1.3k
views
What type of normalization did they use in this article?
normalization TPM r
updated 2.4 years ago by 45k • written 2.4 years ago by ▴ 200
2
votes
4
replies
1.4k
views
MACS2 peak calling
MACS2 peak-calling
updated 2.4 years ago by 11k • written 2.4 years ago by • 0
1
vote
1
reply
756
views
Which type of variant caller should I use in a WES normal cell line sample?
variant-caller WES
updated 2.4 years ago by 89k • written 2.4 years ago by ▴ 170
9
votes
8
replies
2.1k
views
Alignment of case vs. control from different origin
Alignment RNAseq
2.3 years ago by sativus ▴ 20
0
votes
2
replies
1.1k
views
Peaks annotation on bacterial genome
ChIPpeakAnno annotation bacteria
2.4 years ago by Maurice • 0
3
votes
2
replies
1.5k
views
Create customized gene annotation file
reference-genome cellranger
2.3 years ago by rhonddaskl • 0
0
votes
0
replies
497
views
metagenomics data - AMR genes
amr resistome resistance ARG metagenomics
2.4 years ago by aziznasr1920 ▴ 10
1
vote
3
replies
899
views
How to get a comperative result of 2 bed files?
bam cnv bed
updated 2.4 years ago by 166k • written 2.4 years ago by ▴ 10
0
votes
0
replies
612
views
1000G reference panel for LD clumping
LD
2.4 years ago by en_keser • 0
7
votes
25
replies
47k
views
14 follow
CluserProfiler message "No gene can be mapped"
R
updated 2.4 years ago by • 0 • written 7.6 years ago by ▴ 130
165
votes
64
replies
103k
views
39 follow
Selecting Random Pairs From Fastq?
random fastq illumina sequence
updated 20 months ago by 45k • written 14.6 years ago by 4.2k
4
votes
5
replies
15k
views
Take A Subset Of A Fastq Paired-End Sample
paired-end fastq rna-seq illumina
updated 2.4 years ago by 45k • written 12.6 years ago by ▴ 770
2
votes
2
replies
1.1k
views
Forum: Colleges
Colleges india universities
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
3
votes
5
replies
1.3k
views
Concatenating text files based on common indices
Bash Python
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
1
vote
8
replies
2.5k
views
how to create correlation matrix R
pearson-correlation R
2.4 years ago by sata72 • 0
0
votes
0
replies
972
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2 tblastn mmseqs
2.4 years ago by saladi ▴ 30
8
votes
5
replies
1.6k
views
I don't want to believe the Interproscan DB estimated download time.
Interproscan
2.4 years ago by gh • 0
1
vote
7
replies
1.9k
views
RNAseq Data and Pipeline
RNA-Seq DESeq2 Differential-Gene-Expression
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
0
votes
7
replies
2.2k
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 2.4 years ago by 4.8k • written 2.4 years ago by ▴ 40
0
votes
3
replies
2.0k
views
How to make a dotplot for bulk RNA average expression ?
Dotplot RNA-seq
updated 2.4 years ago by ▴ 200 • written 2.4 years ago by • 0
0
votes
3
replies
2.8k
views
Dada2 in Qiime2: losing reads during merging
Qiime2 Chimer Dada2
updated 2.4 years ago by 3.9k • written 2.4 years ago by ▴ 100
0
votes
1
reply
809
views
NCBI Common Taxonomy Tree
phylogenetic-tree comparative-taxonomy ncbi
updated 2.4 years ago by 154k • written 2.4 years ago by • 0
4
votes
6
replies
2.5k
views
Salmon Index
transcriptomics Bulk RNA-sequencing
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 30
1
vote
4
replies
1.7k
views
Expected number of haplotype IDs per path in PHG
PHG
updated 2.4 years ago by 45k • written 2.5 years ago by • 0
0
votes
3
replies
5.2k
views
minimap's SAM file MAPQ value for the unique alignments
minimap MAPQ RNAseq
2.4 years ago by Mo ▴ 50
1
vote
2
replies
844
views
sorting BAM file
BAM
updated 2.4 years ago by 89k • written 2.4 years ago by • 0
0
votes
1
reply
705
views
Search SRA metadata for Histological_Type and Body_Site
sra
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 20
2
votes
3
replies
2.0k
views
NCBI refseq ids to uniprot ids
refseq Uniprot
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
3
votes
3
replies
950
views
Covert multiple short sequence into list of IUPAC motif
sequence
updated 2.4 years ago by 154k • written 2.4 years ago by ▴ 40
5
votes
2
replies
1.1k
views
Graphing Average Expression of Group of Genes
Boxplot R
updated 2.4 years ago by ★ 1.6k • written 2.4 years ago by ▴ 110
0
votes
0
replies
978
views
Converting rds file to h5ad and saving raw counts as X
R seurat
updated 2.4 years ago by 12k • written 2.4 years ago by ▴ 70
0
votes
1
reply
825
views
Seurat: How to get all genes name of a cell ?
seurat
updated 2.4 years ago by ★ 1.9k • written 2.4 years ago by ▴ 690
1
vote
0
replies
631
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
0
votes
0
replies
475
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course RNA-seq pathway
updated 2.4 years ago by 45k • written 2.4 years ago by • 0
121,984 results • Page 252 of 2440
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Answer: Quantification using salmon in alignment-based mode after minimap2 run
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Answer: Corresponding BAM files
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Is this an appropriate command for estimating contaminatin in a germline WGS sample using GATK?
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Comment: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
The program is definitely working. It doesn't matter that it didn't produce `TER` and `END` lines at the end. Those are optional in PDB fil…
Answer: Best set of tools / workflows for predicting the biosynthesis pathways of comple by ehaag ▴ 100
I tried [searching for tools in the NIAID Data Ecosystem][1] and found something that may be relevant. [PathPred][2] is an enzyme catalyzed…
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I did a quick [search for tools in the NIAID Data Ecosystem][1] and found a few that map Illumina short reads onto a reference genome, incl…
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You can get BAM files for 10x single-cell data and they can be found under the `Data Access` tab of the SRA record under the `Original Form…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
All of the genome assemblies are from the LANL compendiu, match accession with GENBANK (>2,000 complete genome assemblies from the 2021 LAN…
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> This project started from my personal need to improve spliced alignment Are there plans to submit these annotations to NCBI/EBI? Are yo…
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Interestingly, HIV/SIV specifically does have quite an elaborate splicing system which regulates translation. However, only one of the spli…
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I'm late to the party but in case someone has the same question: one practical approach is using **rank-based** methods to meta-analyse you…
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I'm late to the party but one practical approach is using **rank-based** methods to meta-analyse your screens, which basically bypass the n…
Comment: convert genome file to transcriptome file by Ales ▴ 50
Should be noted that the gtf/gff and genomic.fna files for HIV only contain CDS annotations of the 9 ORFs and not the full transcripts. Onl…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
just wanted to follow up that to address this specific issue we just released HIV transcriptome annotations of alternative splicing featuri…
Answer: GTF file for HIV strain pNL4-3 by Ales ▴ 50
For anyone stumbling on this. We have recently completed reference-grade annotation for several thousand HIV-1 genomes including the HXB2 (…
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Yes, I found all the barcodes, but could working on WSL affect the basecalling results?
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Since I was running in stub-run mode, the solution was to make unique names for the FASTQC process like this: touch ${sample}_${rea…
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