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758 results • Page 3 of 16
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2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML ncbi entrez-direct
updated 2 days ago by 43k • written 3.9 years ago by • 0
0
votes
6
replies
481
views
Differential Expression Analysis using DESeq2 in R
deseq2 R
updated 14 days ago by 14k • written 14 days ago by • 0
6
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 12 days ago by ▴ 10 • written 2.0 years ago by • 0
10
votes
6
replies
10k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly rna-seq alignment
updated 21 days ago by ★ 5.1k • written 6.0 years ago by ▴ 520
3
votes
6
replies
489
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 5 days ago by ▴ 20 • written 12 days ago by • 0
0
votes
6
replies
218
views
ComplexHeatmap - How to change fontsize of rowAnnotation
ComplexHeatmap
3 hours ago by hannes.bongartz • 0
4
votes
6
replies
806
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 20 days ago by ★ 6.0k • written 24 days ago by ▴ 10
0
votes
6
replies
497
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
updated 23 days ago by • 0 • written 6 weeks ago by ▴ 20
7
votes
6
replies
598
views
Filtering sam or bam file with maximum matching region
crisper-edited alignment match
26 days ago by analyst ▴ 50
2
votes
6
replies
386
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R software error sequencing genome
updated 8 days ago by 142k • written 3.2 years ago by ▴ 10
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 21 days ago by 43k • written 2.4 years ago by ▴ 10
2
votes
5
replies
787
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 27 days ago by ▴ 770 • written 28 days ago by ★ 2.4k
2
votes
5
replies
954
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 18 days ago by ★ 2.0k • written 2.1 years ago by • 0
0
votes
5
replies
6.0k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 27 days ago by • 0 • written 6.5 years ago by ▴ 30
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 26 days ago by 43k • written 10.6 years ago by ▴ 150
0
votes
5
replies
329
views
A question about reference genome for creating the consensus sequence
fasta fa cram genome
9 days ago by me • 0
1
vote
5
replies
493
views
How should I make kallisto indexes?
kallisto
updated 18 days ago by ★ 6.0k • written 4 weeks ago by ▴ 150
0
votes
5
replies
441
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 22 days ago by 142k • written 23 days ago by ▴ 90
2
votes
5
replies
409
views
Importing a fastq file
Fastq
updated 7 days ago by ▴ 120 • written 8 days ago by • 0
3
votes
5
replies
342
views
Generating mpileup file using samtools
mpileup samtools
updated 14 days ago by 21k • written 14 days ago by • 0
0
votes
5
replies
428
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
23 days ago by njornet ▴ 20
1
vote
5
replies
271
views
Reconstruction of locus, order contigs
contigs cluster alignment locus
updated 7 hours ago by ★ 2.0k • written 1 day ago by • 0
0
votes
5
replies
279
views
Percentage coverage of reference genome by de novo genome
SAMtools BWA alignment ddRAD
updated 9 days ago by 21k • written 9 days ago by • 0
2
votes
5
replies
540
views
Marking duplicates using UMIs
Deduplication UMI
updated 25 days ago by 19k • written 27 days ago by • 0
8
votes
5
replies
6.5k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
3
votes
5
replies
397
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
14 days ago by Maverick ▴ 10
0
votes
5
replies
281
views
bbmerge (bbmap) ~ error with insert size file output
bbtools bbmerge bbmap
updated 2 days ago by 142k • written 2 days ago by • 0
3
votes
5
replies
352
views
Per base sequence content error in RNAseq analysis
RNA-seq analysis
updated 25 days ago by 142k • written 25 days ago by • 0
1
vote
5
replies
372
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex bwt
updated 9 days ago by 54k • written 10 days ago by • 0
1
vote
5
replies
643
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 24 days ago by • 0 • written 3 months ago by • 0
3
votes
5
replies
638
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
25 days ago by n_navy • 0
4
votes
5
replies
4.3k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 1 day ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 9 days ago by • 0 • written 5.1 years ago by ★ 1.8k
2
votes
5
replies
425
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
21 days ago by Lada ▴ 30
1
vote
5
replies
808
views
RNA seq differential expression analysis
RNA-seq normalization
updated 28 days ago by ★ 1.7k • written 29 days ago by • 0
5
votes
5
replies
341
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 15 days ago by ▴ 40 • written 15 days ago by ▴ 150
1
vote
5
replies
799
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator IGV
written 6 months ago by ▴ 30
0
votes
5
replies
434
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 14 days ago by ▴ 200 • written 15 days ago by • 0
2
votes
5
replies
540
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
19 days ago by ashaneev07 ▴ 20
5
votes
5
replies
666
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 14 days ago by • 0 • written 22 days ago by ★ 3.9k
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
2 days ago by Arton ▴ 10
0
votes
5
replies
427
views
Telescope issue
Telescope RNA-seq
updated 16 days ago by 142k • written 17 days ago by • 0
1
vote
5
replies
499
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
24 days ago by anasjamshed ▴ 120
1
vote
5
replies
351
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 11 days ago by 43k • written 11 days ago by • 0
1
vote
5
replies
385
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
14 days ago by Riccardo ▴ 10
1
vote
5
replies
249
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq deseq2
updated 1 day ago by 43k • written 1 day ago by • 0
2
votes
5
replies
493
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 3 days ago by 43k • written 9 days ago by • 0
2
votes
5
replies
645
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis MEGA
updated 27 days ago by ★ 27k • written 28 days ago by • 0
1
vote
5
replies
215
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos atacseq
updated 2 days ago by 161k • written 2 days ago by ▴ 50
758 results • Page 3 of 16
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Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
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Recent Replies
Comment: How to handle duplicated genes in TCGA data? by Ngrin • 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2 by swbarnes2 14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot by LauferVA 4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
Answer: GG Sankey plot by bk11 ★ 2.5k
You need to change your data table into a 'long' format. You can do something like this- GOs_childs_recursive <- GOs_childs_recursive …
Answer: Trimming tool by ntsopoul ▴ 60
I use Trim Galore which automatically recognizes adaptors. https://github.com/FelixKrueger/TrimGalore Here is the script I am using for…
Answer: Trimming tool by GenoMax 142k
There are plenty. `bbduk.sh` from BBMap suite (https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbduk-guide/ )…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by bk11 ★ 2.5k
Please check out [in this link.][1] [1]: https://github.com/jokergoo/ComplexHeatmap/issues/349
Comment: Reconstruction of locus, order contigs by dthorbur ★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: how to treat the replicates while performing WGCNA by andres.firrincieli 3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated by alanh ▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data? by Zhenyu Zhang ★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs by BATMAN • 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
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