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1,000 results • Page 3 of 20
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0
votes
1
reply
161
views
Can diamond prepdb be used to make a taxonomically aware database?
blast diamond taxonomy
updated 4 days ago by 142k • written 4 days ago by • 0
0
votes
1
reply
152
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences Demuxlet
updated 4 days ago by 43k • written 4 days ago by • 0
2
votes
5
replies
497
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
1
vote
3
replies
436
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE BAM SAM flag paired-end
4 days ago by kalavattam ▴ 190
1
vote
2
replies
269
views
How to interpret infinite odds ratio?
statistics
4 days ago by Lukas • 0
1
vote
2
replies
181
views
Duplicated sequence samtools
bowtie2 samtools
updated 4 days ago by 142k • written 4 days ago by • 0
0
votes
0
replies
105
views
reference-free assembly error assessment tools
assembly
4 days ago by lagartija ▴ 160
2
votes
4
replies
298
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
3 days ago by Esraa • 0
0
votes
1
reply
142
views
Splitting Seurat object by sample layers
seurat
updated 4 days ago by 43k • written 4 days ago by ▴ 10
0
votes
4
replies
262
views
Galaxy StringTie error
stringtie galaxy
4 days ago by trkfs • 0
0
votes
0
replies
105
views
dbNSFP sift scores integration
SIFT VEP dbNSFP
4 days ago by atariw ▴ 10
0
votes
1
reply
157
views
Mouse ribosome sequences in fasta format
fasta mm10 rRNA
updated 4 days ago by 142k • written 5 days ago by ▴ 100
1
vote
4
replies
347
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus annotation assembly genome
updated 3 days ago by 8.6k • written 4 days ago by ▴ 30
0
votes
1
reply
162
views
consensus sequence calling
consensus
updated 4 days ago by ★ 2.5k • written 4 days ago by • 0
0
votes
3
replies
192
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat single-cell scRNA-seq R
updated 4 days ago by 43k • written 4 days ago by • 0
3
votes
2
replies
286
views
imputation through beagle
panel beagle reference imputation
4 days ago by analyst ▴ 50
0
votes
0
replies
88
views
Empty kernel in SEACells model
single-cell scanpy seacells python anndata
4 days ago by JACKY ▴ 140
0
votes
1
reply
536
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
updated 4 days ago by ▴ 300 • written 28 days ago by • 0
3
votes
1
reply
218
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair samtools alignment
updated 5 days ago by ▴ 300 • written 9 days ago by ▴ 40
0
votes
0
replies
104
views
Reference panel of normals for ensembl named refgenome
Mutect2
5 days ago by gernophil ▴ 80
1
vote
0
replies
97
views
Producing sequence for splicing isoforms
isoform rMATs splicing alternative SplAdder
5 days ago by tomas4482 ▴ 400
2
votes
6
replies
388
views
BWA alignment
Samtools bam
updated 3 days ago by ▴ 260 • written 5 days ago by • 0
3
votes
2
replies
194
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 5 days ago by 82k • written 5 days ago by • 0
0
votes
1
reply
157
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence university assembly protein genomics
updated 5 days ago by 8.5k • written 5 days ago by • 0
0
votes
1
reply
247
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 4 days ago by 43k • written 8 days ago by • 0
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by • 0 • written 4.8 years ago by ▴ 60
0
votes
1
reply
196
views
Generating .bed file and .map file for polyploid vcf file through plink
bed polyploid map plink
updated 5 days ago by 10k • written 10 days ago by ▴ 50
0
votes
0
replies
111
views
lncRNA
tcga lncrna
5 days ago by jain72744 ▴ 10
0
votes
1
reply
244
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA RNA-seq Nomalization Microarray
updated 5 days ago by ★ 1.2k • written 8 days ago by ▴ 10
2
votes
5
replies
578
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 5 days ago by ▴ 40 • written 14 days ago by ▴ 30
1
vote
2
replies
363
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq limma RNA-seq removeBatchEffect batch-effect
updated 4 days ago by 43k • written 5 days ago by • 0
2
votes
1
reply
264
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
updated 5 days ago by ▴ 210 • written 7 days ago by ▴ 10
0
votes
2
replies
210
views
Output file of samtools flagstat empty
samtools-flagstat
updated 5 days ago by 6.4k • written 5 days ago by • 0
2
votes
8
replies
385
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 5 days ago by 161k • written 6 days ago by ▴ 100
0
votes
1
reply
234
views
input file in rmats
rmats
updated 6 days ago by ▴ 140 • written 8 days ago by • 0
3
votes
3
replies
365
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 4 days ago by ▴ 140 • written 7 days ago by • 0
6
votes
7
replies
392
views
Longest transcript variant per gene
transcript longest variant orthofinder
5 days ago by sansan_96 ▴ 90
2
votes
3
replies
286
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio Cibersort R
5 days ago by Azra ▴ 10
2
votes
1
reply
234
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 6 days ago by 161k • written 7 days ago by ▴ 70
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 days ago by • 0 • written 5.7 years ago by ▴ 20
0
votes
4
replies
407
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
5 days ago by beginner123 • 0
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated 6 days ago by • 0 • written 6.5 years ago by ▴ 130
0
votes
2
replies
232
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated java.nio.bufferunderflowexception haplotypecaller bqsr
5 days ago by analyst ▴ 50
0
votes
6
replies
426
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf genomics plink
updated 4 days ago by 43k • written 7 days ago by • 0
0
votes
11
replies
545
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
5 days ago by Tuck898 • 0
3
votes
3
replies
284
views
what is another word for a BLAST "hit"?
blast alignment
7 days ago by dec986 ▴ 380
0
votes
1
reply
205
views
extract viral protein of interest from 10k whole viral genomes
nBLAST viral-genome
updated 7 days ago by 43k • written 7 days ago by • 0
0
votes
0
replies
165
views
Marker Features variance by cluster, sample, and treatment group
Seurat scATAC-seq ArchR
updated 7 days ago by 43k • written 7 days ago by • 0
1
vote
3
replies
287
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk vcf liftover
updated 7 days ago by 43k • written 7 days ago by ▴ 260
9
votes
6
replies
12k
views
samtools tview symbols
samtools
updated 8.8 years ago by 12k • written 8.8 years ago by ★ 1.4k
1,000 results • Page 3 of 20
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Recent Replies
Answer: RNAseq coverage vs depth for transcript isoform expression? by Gordon Smyth ★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Our resul…
Comment: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA by mavy ▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object by Alex Reynolds 35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF) by aidangcruickshank ▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
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.
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