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186 results • Page 3 of 4
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2
votes
5
replies
268
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 3 days ago by 8.5k • written 3 days ago by • 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11 Autodock windows MGLTools
updated 2 days ago by 43k • written 13 months ago by • 0
2
votes
4
replies
224
views
Help with IGV abbreviation
igv
updated 2 days ago by 43k • written 3 days ago by • 0
0
votes
1
reply
161
views
How to process Bulk WES data?
WES WGS
updated 3 days ago by 142k • written 3 days ago by • 0
0
votes
1
reply
161
views
Can diamond prepdb be used to make a taxonomically aware database?
blast diamond taxonomy
updated 3 days ago by 142k • written 4 days ago by • 0
0
votes
2
replies
430
views
News: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq variant-calling RNA-seq illumina transcriptomics
4 days ago by David Langenberger 11k
0
votes
1
reply
149
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences Demuxlet
updated 3 days ago by 43k • written 4 days ago by • 0
2
votes
5
replies
492
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 2 days ago by 43k • written 9 days ago by • 0
1
vote
3
replies
434
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
268
views
How to interpret infinite odds ratio?
statistics
3 days ago by Lukas • 0
1
vote
2
replies
179
views
Duplicated sequence samtools
bowtie2 samtools
updated 4 days ago by 142k • written 4 days ago by • 0
0
votes
0
replies
104
views
reference-free assembly error assessment tools
assembly
4 days ago by lagartija ▴ 160
2
votes
4
replies
293
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
2 days ago by Esraa • 0
2
votes
0
replies
141
views
Herald: The Biostar Herald for Monday, May 13, 2024
herald
4 days ago by Biostar 2.8k
0
votes
1
reply
142
views
Splitting Seurat object by sample layers
seurat
updated 3 days ago by 43k • written 4 days ago by ▴ 10
0
votes
4
replies
258
views
Galaxy StringTie error
stringtie galaxy
3 days ago by trkfs • 0
0
votes
0
replies
103
views
dbNSFP sift scores integration
SIFT VEP dbNSFP
4 days ago by atariw ▴ 10
0
votes
1
reply
154
views
Mouse ribosome sequences in fasta format
fasta mm10 rRNA
updated 4 days ago by 142k • written 4 days ago by ▴ 100
1
vote
4
replies
345
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus annotation assembly genome
updated 2 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 3 days ago by 43k • written 4 days ago by • 0
3
votes
2
replies
279
views
imputation through beagle
panel beagle reference imputation
3 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
534
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
216
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair samtools alignment
updated 4 days ago by ▴ 300 • written 8 days ago by ▴ 40
0
votes
0
replies
101
views
Reference panel of normals for ensembl named refgenome
Mutect2
4 days ago by gernophil ▴ 80
1
vote
0
replies
97
views
Producing sequence for splicing isoforms
isoform rMATs splicing alternative SplAdder
4 days ago by tomas4482 ▴ 400
2
votes
6
replies
382
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
3
votes
2
replies
189
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 4 days ago by 82k • written 4 days ago by • 0
0
votes
1
reply
157
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence university assembly protein genomics
updated 4 days ago by 8.5k • written 5 days ago by • 0
0
votes
1
reply
246
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 3 days ago by 43k • written 8 days ago by • 0
2
votes
14
replies
2.9k
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
194
views
Generating .bed file and .map file for polyploid vcf file through plink
bed polyploid map plink
updated 4 days ago by 10k • written 9 days ago by ▴ 50
0
votes
0
replies
110
views
lncRNA
tcga lncrna
4 days ago by jain72744 ▴ 10
0
votes
1
reply
242
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA RNA-seq Nomalization Microarray
updated 4 days ago by ★ 1.2k • written 7 days ago by ▴ 10
2
votes
5
replies
568
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
359
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
263
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 4 days ago by 6.4k • written 5 days ago by • 0
2
votes
8
replies
379
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 5 days ago by 161k • written 5 days ago by ▴ 100
0
votes
0
replies
128
views
News: Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore RNAseq
5 days ago by carlopecoraro2 ★ 2.5k
0
votes
1
reply
233
views
input file in rmats
rmats
updated 5 days ago by ▴ 140 • written 7 days ago by • 0
3
votes
3
replies
362
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 3 days ago by ▴ 140 • written 6 days ago by • 0
6
votes
7
replies
387
views
Longest transcript variant per gene
transcript longest variant orthofinder
5 days ago by sansan_96 ▴ 90
2
votes
3
replies
280
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio Cibersort R
4 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 6 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
399
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 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
231
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated java.nio.bufferunderflowexception haplotypecaller bqsr
4 days ago by analyst ▴ 50
186 results • Page 3 of 4
Recent Votes
Answer: How to download dbSNP153 vcf files in hg19/GRCH37 version
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Answer: TFs and Gene databases
A: Is there a software that can compare phylogenetic trees to each othe (face to fa
Comment: Differentially Expressed Genes between two conditions (scRNA, single GEO dataset
Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
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Recent Replies
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: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
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.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by hannes.bongartz • 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation by Ram 43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index by Rob 6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
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