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804 results • Page 4 of 17
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3
votes
4
replies
415
views
Why gatk VariantAnnotator required bam and coverage files
gatk VariantAnnotator
21 days ago by QX • 0
3
votes
3
replies
751
views
KissDE and batch effect
kissDE kissplice
24 days ago by david.b.rombaut ▴ 10
3
votes
2
replies
419
views
Extract protein sequence
fasta alignment blast
16 days ago by anna ▴ 20
3
votes
3
replies
367
views
Sequence read length shorter than flow cell specification
illumina NGS sequencing
updated 21 days ago by 14k • written 21 days ago by • 0
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk genomicsdbimport
updated 14 days ago by • 0 • written 5.1 years ago by 11k
3
votes
3
replies
368
views
genome assembly records not present in assembly_summary.txt
ncbi bacteria assembly
updated 20 days ago by 142k • written 20 days ago by ▴ 10
3
votes
1
reply
213
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair samtools alignment
updated 3 days ago by ▴ 300 • written 8 days ago by ▴ 40
3
votes
2
replies
167
views
Details on salmon index
Salmon
updated 13 hours ago by 6.6k • written 20 hours ago by • 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 29 days ago by 43k • written 4.5 years ago by ▴ 10
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression R limma batch-effect model-matrix
updated 28 days ago by 43k • written 7.3 years ago by ▴ 20
2
votes
5
replies
423
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq assembly transcriptome contamination
20 days ago by Lada ▴ 30
2
votes
4
replies
719
views
Count all variants from vcf file
variants vcf Count
updated 9 days ago by 161k • written 21 months ago by • 0
2
votes
3
replies
500
views
Sheep reference genome remapping coordinates
reference remap sheep coordinates genome
28 days ago by valentinatsar • 0
2
votes
3
replies
322
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus annotation assembly genome
updated 13 days ago by ★ 2.0k • written 13 days ago by ▴ 30
2
votes
5
replies
566
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 4 days ago by ▴ 40 • written 13 days ago by ▴ 30
2
votes
3
replies
844
views
Issues with Mixture file when using CIBERSORTx
Deconvolution CIBERSORTx
updated 12 days ago by • 0 • written 7 months ago by • 0
2
votes
5
replies
404
views
Importing a fastq file
Fastq
updated 7 days ago by ▴ 120 • written 7 days ago by • 0
2
votes
3
replies
272
views
Finding variants within a subset of a BAM file
variant calling
2 days ago by ramiro.barrantes • 0
2
votes
4
replies
389
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 23 days ago by 14k • written 24 days ago by • 0
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell RNA-Seq batch-effect
updated 29 days ago by 43k • written 6.0 years ago by ▴ 60
2
votes
7
replies
1.4k
views
6 follow
Differential Expression using Isoseq-supplemented reference transcriptome
RNA-Seq Salmon Isoseq
updated 18 days ago by ★ 7.2k • written 8 months ago by ▴ 10
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq batch-effect
updated 28 days ago by 43k • written 5.1 years ago by ▴ 60
2
votes
1
reply
232
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 5 days ago by 161k • written 5 days ago by ▴ 70
2
votes
2
replies
310
views
p-value in CIBERSORT
CIBERSORT p-value
15 days ago by michelafrancesconi9 ▴ 20
2
votes
2
replies
217
views
MA plot of shrunken fold change
MA-plot Deseq2
updated 16 days ago by 82k • written 16 days ago by • 0
2
votes
5
replies
266
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
5
replies
536
views
Fetch table from clinvar database according to a list of rsid
python clinvar perl
18 days ago by ashaneev07 ▴ 20
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 28 days ago by 43k • written 4.8 years ago by ▴ 20
2
votes
2
replies
428
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression edgeR
28 days ago by nhaus ▴ 360
2
votes
2
replies
242
views
Raw counts using stringtie
stringtie RNA-seq
updated 13 days ago by 142k • written 13 days ago by • 0
2
votes
3
replies
208
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC RNA-Seq
updated 2 days ago by 43k • written 2 days ago by • 0
2
votes
6
replies
3.8k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell RNAseq DE Analysis Treatment Control
updated 21 days ago by 82k • written 3.9 years ago by ▴ 280
2
votes
5
replies
535
views
Marking duplicates using UMIs
Deduplication UMI
updated 24 days ago by 19k • written 26 days ago by • 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 2 days ago by • 0 • written 4.8 years ago by ▴ 60
2
votes
0
replies
165
views
Herald: The Biostar Herald for Monday, May 06, 2024
herald
10 days ago by Biostar 2.8k
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 8 days ago by • 0 • written 5.1 years ago by ★ 1.8k
2
votes
2
replies
393
views
Hide positions in alignment with 99% "–" characters to ignore single sequence insertions?
alignment gaps
updated 19 days ago by ▴ 770 • written 21 days ago by • 0
2
votes
3
replies
995
views
Method to detect genome doubling
CNV genome doubling
updated 24 days ago by 4.2k • written 4.5 years ago by ▴ 750
2
votes
2
replies
195
views
Genome Visualization Tools
bacterial genome
updated 2 days ago by 142k • written 2 days ago by ▴ 10
2
votes
9
replies
692
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 1 day ago by 161k • written 9 days ago by • 0
2
votes
3
replies
183
views
ggrepel function: geom_text_repel()
ggplot2 ggrepel R
updated 6 hours ago by 43k • written 1 day ago by ▴ 20
2
votes
0
replies
155
views
News: course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics SNPs LocalAdaptation GIS
7 days ago by carlopecoraro2 ★ 2.5k
2
votes
7
replies
5.3k
views
6 follow
Memory usage of picard Samsort
Picard SortSam
updated 27 days ago by 82k • written 7.2 years ago by ▴ 80
2
votes
6
replies
377
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
2
votes
4
replies
2.7k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 17 days ago by 9.7k • written 2.0 years ago by ▴ 120
2
votes
3
replies
401
views
Editing Human Reference Genome by adding a CDS
gff agat transcriptome
updated 29 days ago by 54k • written 29 days ago by ▴ 340
2
votes
2
replies
334
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 22 days ago by 43k • written 23 days ago by ▴ 140
2
votes
2
replies
155
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 9 hours ago by 43k • written 12 hours ago by ▴ 130
2
votes
3
replies
276
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio Cibersort R
3 days ago by Azra ▴ 10
2
votes
2
replies
480
views
Using vg gamsort with naive sorting algorithm
gamsort vg
updated 23 days ago by 161k • written 8 months ago by ▴ 80
804 results • Page 4 of 17
Recent Votes
Answer: ggrepel function: geom_text_repel()
Comment: switch off warning in blast command line
Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Answer: Details on salmon index
ATAC-seq sample normalization
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Recent Replies
Comment: How to extract cells of different species after mapping with combined genome? by Tony • 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Nyksubuz ▴ 10
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test by Nyksubuz ▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite by dario.garvan ▴ 520
It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by GenoMax 142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
Comment: Collect dispersed executable files and run them by using bingo. by Ram 43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
Can you try this? library(dplyr) seuratobj@meta.data <- seuratobj@meta.data %>% mutate(seurat_clusters = recode(seurat_clu…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
Thank you for the response but it does not change anything.
Comment: Merge clusters in Seurat UMAP by bk11 ★ 2.4k
I have not tested but you could try something like below- seuratobj$seurat_clusters[seuratobj$seurat_clusters==5]=0 seuratobj$seur…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I know about it, isn't there a simple C++ static binary?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
needle is great! but it does not handle sequences of 100k or so.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by Ram 43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction by txema.heredia ▴ 130
The point is that you need to feed the ambient algorithm a clustering list as input. This way, it checks for genes present in the soup vs g…
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