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182 results • Page 1 of 4
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38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 5 hours ago by ▴ 170 • written 7.1 years ago by ▴ 240
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
6 days ago by vytarasov ▴ 180
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
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
2 days ago by Arton ▴ 10
6
votes
4
replies
266
views
Details on salmon index
Salmon
updated 8 hours ago by 6.6k • written 1 day 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
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 5 days ago by • 0 • written 6.7 years ago by • 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
5
votes
7
replies
489
views
RNA seq analysis
DESeq RNA-seq
2 days ago by Jacek ▴ 20
4
votes
7
replies
435
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA R VARIANCE
updated 9 hours ago by ▴ 130 • written 2 days ago by ▴ 20
4
votes
9
replies
399
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
9 hours ago by Gabriel R. ★ 2.9k
4
votes
7
replies
412
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
3 days ago by Chen • 0
4
votes
1
reply
202
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
3 days ago by J. ▴ 40
4
votes
4
replies
3.0k
views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
updated 3 days ago by • 0 • written 5.1 years ago by • 0
4
votes
5
replies
4.3k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 22 hours ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
3
votes
4
replies
268
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq patch freeze genome
updated 6 hours ago by 22k • written 1 day 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
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
3
votes
4
replies
353
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR masspec uORF peptide
updated 1 day ago by 142k • written 1 day ago by 161k
3
votes
6
replies
489
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 4 days ago by ▴ 20 • written 12 days ago by • 0
3
votes
3
replies
224
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm ChIP-seq consensus peaks
updated 1 day ago by 82k • written 2 days ago by • 0
3
votes
3
replies
268
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 4 days ago by 43k • written 17 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
3
votes
3
replies
188
views
getting exon coordinates
genomics
updated 1 day ago by 43k • written 1 day ago by • 0
3
votes
2
replies
281
views
imputation through beagle
panel beagle reference imputation
3 days ago by analyst ▴ 50
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
2
replies
196
views
genome finishing
finishing genome
updated 2 days ago by ▴ 20 • written 2 days ago by • 0
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
2
votes
4
replies
294
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
2 days ago by Esraa • 0
2
votes
6
replies
384
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
2
votes
9
replies
695
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 2 days ago by 161k • written 10 days ago by • 0
2
votes
11
replies
647
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio DEG limma
14 hours ago by egascon • 0
2
votes
4
replies
224
views
Help with IGV abbreviation
igv
updated 3 days ago by 43k • written 3 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
2
votes
2
replies
196
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 1 day ago by 43k • written 1 day ago by ▴ 130
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
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
2
votes
0
replies
141
views
Herald: The Biostar Herald for Monday, May 13, 2024
herald
4 days ago by Biostar 2.8k
2
votes
2
replies
183
views
Cannot install bwa-mem2 via conda
conda mamba python
updated 1 day ago by 43k • written 2 days ago by • 0
2
votes
3
replies
219
views
ggrepel function: geom_text_repel()
ggplot2 ggrepel R
updated 23 hours ago by 43k • written 1 day ago by ▴ 20
2
votes
4
replies
269
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell seurat 10XGenomics scRNAseq
updated 2 days ago by ▴ 90 • written 2 days ago by ▴ 20
2
votes
3
replies
276
views
Finding variants within a subset of a BAM file
variant calling
3 days ago by ramiro.barrantes • 0
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq alignment RNA-Seq featureCounts STAR
updated 4 days ago by ▴ 340 • written 4.9 years ago by ▴ 70
2
votes
2
replies
203
views
Genome Visualization Tools
bacterial genome
updated 3 days ago by 142k • written 3 days ago by ▴ 10
2
votes
3
replies
213
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC RNA-Seq
updated 3 days ago by 43k • written 3 days 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
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
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
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
1
vote
0
replies
97
views
Producing sequence for splicing isoforms
isoform rMATs splicing alternative SplAdder
4 days ago by tomas4482 ▴ 400
182 results • Page 1 of 4
Recent Votes
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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
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Recent Replies
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: 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.
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