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698 results • Page 3 of 14
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4
votes
6
replies
820
views
7 follow
Heatmap and rna-seq
RNA-Seq Heatmap
updated 24 days ago by ★ 6.0k • written 28 days ago by ▴ 10
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R software error sequencing genome
updated 12 days ago by 142k • written 3.2 years ago by ▴ 10
0
votes
5
replies
316
views
Percentage coverage of reference genome by de novo genome
SAMtools BWA alignment ddRAD
updated 13 days ago by 21k • written 13 days ago by • 0
1
vote
5
replies
411
views
Introduce SNPs on FASTA
simulation snps haplotypes pharmacogenetics
18 days ago by Riccardo ▴ 10
0
votes
5
replies
364
views
A question about reference genome for creating the consensus sequence
fasta fa cram genome
12 days ago by me • 0
0
votes
5
replies
214
views
Why most genes have high padj values
RNA-seq DEG
updated 21 hours ago by 43k • written 1 day ago by • 0
1
vote
5
replies
375
views
Reconstruction of locus, order contigs
contigs cluster alignment locus
updated 3 days ago by ★ 2.0k • written 4 days ago by • 0
5
votes
5
replies
354
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
13 days ago by Chris ▴ 280
3
votes
5
replies
422
views
Converting CRAM to FastQ
GATK samtools cram SamToFastq fastq
17 days ago by Maverick ▴ 10
1
vote
5
replies
813
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator IGV
written 6 months ago by ▴ 30
0
votes
5
replies
315
views
calculating genomic coverage/ base overlap in R
genomics
updated 3 days ago by ★ 1.2k • written 6 days ago by • 0
1
vote
5
replies
507
views
How should I make kallisto indexes?
kallisto
updated 21 days ago by ★ 6.0k • written 5 weeks ago by ▴ 150
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 9 days ago by • 0 • written 6.7 years ago by • 0
5
votes
5
replies
682
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 17 days ago by • 0 • written 26 days ago by ★ 3.9k
0
votes
5
replies
342
views
how to treat the replicates while performing WGCNA
clustering WGCNA replicates
15 hours ago by mavy ▴ 10
2
votes
5
replies
556
views
Marking duplicates using UMIs
Deduplication UMI
updated 29 days ago by 19k • written 4 weeks ago by • 0
2
votes
5
replies
523
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 6 days ago by 43k • written 12 days ago by • 0
3
votes
5
replies
653
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
29 days ago by n_navy • 0
0
votes
5
replies
444
views
Telescope issue
Telescope RNA-seq
updated 19 days ago by 142k • written 20 days ago by • 0
1
vote
5
replies
386
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 15 days ago by 43k • written 15 days ago by • 0
4
votes
5
replies
4.4k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 4 days ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
0
votes
5
replies
363
views
How to convert normalized BigWig file to count matrix?
count-matrix BigWig
8 days ago by feather-W • 0
0
votes
5
replies
352
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
8 days ago by SilhouetteQ • 0
0
votes
5
replies
299
views
bbmerge (bbmap) ~ error with insert size file output
bbtools bbmerge bbmap
updated 5 days ago by 142k • written 6 days ago by • 0
5
votes
5
replies
368
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA DADA2 metabarcoding
updated 18 days ago by ▴ 40 • written 19 days ago by ▴ 150
2
votes
5
replies
555
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
22 days ago by ashaneev07 ▴ 20
2
votes
5
replies
10k
views
Find Corresponding Author: Doi Metadata?
updated 29 days ago by 43k • written 10.6 years ago by ▴ 150
2
votes
5
replies
447
views
Importing a fastq file
Fastq
updated 11 days ago by ▴ 120 • written 12 days ago by • 0
2
votes
5
replies
962
views
Retrieval of Active site information programmatically
Catalytic Python Active PDB site Site
updated 21 days ago by ★ 2.0k • written 2.1 years ago by • 0
3
votes
5
replies
359
views
Generating mpileup file using samtools
mpileup samtools
updated 18 days ago by 21k • written 18 days ago by • 0
2
votes
5
replies
292
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 7 days ago by 8.5k • written 7 days ago by • 0
0
votes
5
replies
449
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 26 days ago by 142k • written 26 days ago by ▴ 90
0
votes
5
replies
461
views
6 follow
What purposes can TPM values be used for?
RNA-seq TPM Normalization DESeq2
updated 18 days ago by ▴ 200 • written 18 days ago by • 0
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
6 days ago by Arton ▴ 10
2
votes
5
replies
436
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
25 days ago by Lada ▴ 30
1
vote
5
replies
527
views
DYH17 Structure Prediction
BLAST Protein-Structure-Prediction
27 days ago by anasjamshed ▴ 120
0
votes
5
replies
409
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 17 days ago by 10k • written 17 days ago by ▴ 750
2
votes
5
replies
609
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 8 days ago by ▴ 40 • written 17 days ago by ▴ 30
1
vote
5
replies
279
views
Annotating file using bcftools
annotation plink bcftools
4 days ago by kl ▴ 10
1
vote
5
replies
663
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode MGI DNBelab single-cell
updated 27 days ago by • 0 • written 4 months ago by • 0
4
votes
5
replies
467
views
Figures are disappeared from html report of SnpEff
HTML SnpEff
22 days ago by analyst ▴ 50
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 12 days ago by ▴ 90 • written 6.4 years ago by ▴ 60
1
vote
5
replies
488
views
HCL database download
HCL
updated 13 days ago by 43k • written 17 days ago by ▴ 20
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 12 days ago by • 0 • written 5.1 years ago by ★ 1.8k
8
votes
5
replies
6.6k
views
ISCN annotation for SV/CN VCF files
SV
written 8 months ago by ▴ 60
1
vote
5
replies
332
views
Can I perform a correlation test with 3 biological replicates per condition?
RNA-Seq deseq2
updated 4 days ago by 43k • written 5 days ago by • 0
0
votes
5
replies
472
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 23 days ago by 100k • written 27 days ago by ▴ 10
1
vote
5
replies
415
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex bwt
updated 13 days ago by 54k • written 14 days ago by • 0
0
votes
5
replies
440
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap alignment minimap2 GRCh38 assembly
27 days ago by njornet ▴ 20
1
vote
5
replies
233
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos atacseq
updated 5 days ago by 161k • written 5 days ago by ▴ 50
698 results • Page 3 of 14
Recent Votes
A: RSeQC Output from infer_experiment.py - what does it mean?
A: findOverlaps function in R
Comment: What marks a De-Novo Genome assembly as FAILED?
A: How to extract specific chromosome from vcf file
A: How To Filter Mapped Reads With Samtools
C: Filtering A Sam File For Quality Scores
A: Filtering A Sam File For Quality Scores
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Recent Replies
Comment: Generating a Bed file from a Fasta file by Pierre Lindenbaum 161k
there is not enough information. you have to show us the command you used, a snapshot of your fasta...
Comment: Practical Haplotype Graph v2 not finding correct paths by beantkapoor16 ▴ 10
That's great. I will test it and let you know how it goes. Thank you.
Comment: Generating a Bed file from a Fasta file by pirku • 0
I tried running BLAT, but the output looks like this. Seems like none of the sequences were mapped/aligned match mis- rep. N's Q gap…
Comment: Where to find old version of GATK best practice by GenoMax 142k
You could try and look up a snapshot of the page(s) - https://web.archive.org/ Which specific best practice are you referring to? https:/…
Comment: Generating a Bed file from a Fasta file by Pierre Lindenbaum 161k
you could run blast or any other aligner to get the coordinate(s) of your fasta on a reference genome.
Answer: Running STRUCTURE from command line by Arthur • 0
If it cans help, I got the same error message : There were errors in the input file (listed above). According to "mainparams" the inp…
Comment: CreateSeuratObject taking very long by Nitin Narwade ★ 1.6k
I am not sure whether it will speedup the conversion but you can give it a try. convert your dataframe into a sparse matrix before creatin…
Comment: Practical Haplotype Graph v2 not finding correct paths by pjb39 ▴ 210
The timing for your question is excellent. The fix was released yesterday.
Comment: vcf phasing by WouterDeCoster 47k
> I observed that it doesn't phase genotypes labeled as 0/0 How could such a genotype even be phased?
Comment: Super ehancers by Oburah • 0
Well-noted however just wondering what you me by GFF being shorter. Thank you![See the screeshot snap of the gff file][1] [1]: /media/i…
Comment: What marks a De-Novo Genome assembly as FAILED? by Umer ▴ 50
I know illumina will only give me high-quality contigs. the samples which are to be sequenced with Long_Short read sequence will be used as…
Comment: What marks a De-Novo Genome assembly as FAILED? by Umer ▴ 50
Hi, Thank you for a detailed responce. Let me add some more informations. Long-Read is ~75X coverage. Short-Read is ~100X coverage. **For…
Comment: Pruning Phylogenetic Trees and Bootstrap Values by Klaus S ▴ 160
The best is to prune the tree and also the bootstrap trees and afterwards re-assign the bootstrap values to the tree. The bootstrap values …
Comment: What is the amount of sequencing data produced annually? by Mohamed • 0
Here's a more neat version of the plot generated while writing my dissertation: ![enter image description here][1] [1]: https://raw.gi…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 130
what a pity...
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