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191 results • Page 3 of 4
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0
votes
0
replies
104
views
reference-free assembly error assessment tools
assembly
3 days ago by lagartija ▴ 160
2
votes
4
replies
291
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
1 day ago by Esraa • 0
2
votes
0
replies
141
views
Herald: The Biostar Herald for Monday, May 13, 2024
herald
3 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 3 days ago by ▴ 10
0
votes
4
replies
254
views
Galaxy StringTie error
stringtie galaxy
2 days ago by trkfs • 0
0
votes
0
replies
102
views
dbNSFP sift scores integration
SIFT VEP dbNSFP
3 days ago by atariw ▴ 10
0
votes
1
reply
151
views
Mouse ribosome sequences in fasta format
fasta mm10 rRNA
updated 3 days ago by 142k • written 4 days ago by ▴ 100
1
vote
4
replies
340
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 3 days ago by ▴ 30
0
votes
1
reply
161
views
consensus sequence calling
consensus
updated 3 days ago by ★ 2.4k • written 3 days ago by • 0
0
votes
3
replies
190
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 3 days ago by • 0
3
votes
2
replies
274
views
imputation through beagle
panel beagle reference imputation
2 days ago by analyst ▴ 50
0
votes
0
replies
88
views
Empty kernel in SEACells model
single-cell scanpy seacells python anndata
3 days ago by JACKY ▴ 140
0
votes
1
reply
528
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
updated 3 days ago by ▴ 300 • written 27 days ago by • 0
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
0
votes
0
replies
101
views
Reference panel of normals for ensembl named refgenome
Mutect2
3 days ago by gernophil ▴ 80
1
vote
0
replies
95
views
Producing sequence for splicing isoforms
isoform rMATs splicing alternative SplAdder
3 days ago by tomas4482 ▴ 400
2
votes
6
replies
375
views
BWA alignment
Samtools bam
updated 1 day ago by ▴ 260 • written 4 days ago by • 0
3
votes
2
replies
186
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 3 days ago by 82k • written 3 days ago by • 0
0
votes
1
reply
156
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence university assembly protein genomics
updated 3 days ago by 8.5k • written 4 days ago by • 0
0
votes
1
reply
244
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 3 days ago by 43k • written 7 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
0
votes
1
reply
193
views
Generating .bed file and .map file for polyploid vcf file through plink
bed polyploid map plink
updated 3 days ago by 10k • written 8 days ago by ▴ 50
0
votes
0
replies
109
views
lncRNA
tcga lncrna
3 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 6 days ago by ▴ 10
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
1
vote
2
replies
356
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 3 days ago by 43k • written 4 days ago by • 0
2
votes
1
reply
256
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
updated 4 days ago by ▴ 210 • written 6 days ago by ▴ 10
0
votes
2
replies
206
views
Output file of samtools flagstat empty
samtools-flagstat
updated 3 days ago by 6.4k • written 4 days ago by • 0
2
votes
8
replies
370
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 4 days ago by 161k • written 4 days ago by ▴ 100
0
votes
0
replies
127
views
News: Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore RNAseq
4 days ago by carlopecoraro2 ★ 2.5k
0
votes
1
reply
229
views
input file in rmats
rmats
updated 4 days ago by ▴ 140 • written 6 days ago by • 0
3
votes
3
replies
356
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 3 days ago by ▴ 140 • written 6 days ago by • 0
6
votes
7
replies
382
views
Longest transcript variant per gene
transcript longest variant orthofinder
4 days ago by sansan_96 ▴ 90
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
1
reply
231
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 5 days ago by 161k • written 5 days ago by ▴ 70
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 5 days ago by • 0 • written 5.7 years ago by ▴ 20
0
votes
4
replies
393
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
3 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 5 days ago by • 0 • written 6.5 years ago by ▴ 130
0
votes
2
replies
228
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated java.nio.bufferunderflowexception haplotypecaller bqsr
3 days ago by analyst ▴ 50
0
votes
6
replies
417
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf genomics plink
updated 3 days ago by 43k • written 6 days ago by • 0
0
votes
11
replies
531
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
4 days ago by Tuck898 • 0
3
votes
3
replies
278
views
what is another word for a BLAST "hit"?
blast alignment
6 days ago by dec986 ▴ 380
0
votes
1
reply
202
views
extract viral protein of interest from 10k whole viral genomes
nBLAST viral-genome
updated 6 days ago by 43k • written 6 days ago by • 0
0
votes
0
replies
163
views
Marker Features variance by cluster, sample, and treatment group
Seurat scATAC-seq ArchR
updated 6 days ago by 43k • written 6 days ago by • 0
1
vote
3
replies
281
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk vcf liftover
updated 6 days ago by 43k • written 6 days ago by ▴ 260
2
votes
9
replies
690
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
0
votes
5
replies
316
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
3 days ago by SilhouetteQ • 0
0
votes
1
reply
187
views
Alignment of samples with spike-in
alignment multimapping RNA-seq ChIP-seq spike-in
updated 6 days ago by 142k • written 6 days ago by • 0
0
votes
2
replies
292
views
How are score_weights calculated in this code?
single-cell
5 days ago by carolofharvest ▴ 40
0
votes
1
reply
222
views
How to convert Haps file to vcf file?
pre-phasing GWAS imputation
updated 6 days ago by ▴ 750 • written 6 days ago by • 0
191 results • Page 3 of 4
Recent Votes
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
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Comment: Can I perform a correlation test with 3 biological replicates per condition?
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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…
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by swbarnes2 14k
Wait, so the magnitudes of the PCs are in the thousands? That's not normal for RNASeq.
Comment: Help with VG Toolkit: VCF Output is Empty by Jordan M Eizenga ▴ 460
What do you get if you use `vg stats -a` on the GAM file?
Comment: About runing Pilon on individual chromosomes when polish draft genome assembly by sansan_96 ▴ 90
Hello, What approach could you recommend for a large genome (3Gb) with about 10k scaffolds? I'm having problems with RAM when processing t…
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