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180 results • Page 1 of 4
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9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
2 days ago by vytarasov ▴ 180
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 6 days ago by 161k • written 5.8 years ago by ▴ 180
13
votes
14
replies
849
views
High Malat-1 expression in single cell data
single-cell
updated 5 days ago by ▴ 40 • written 14 days ago by ▴ 40
10
votes
14
replies
689
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 6 days ago by 142k • written 11 days ago by • 0
2
votes
13
replies
2.8k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 9 hours ago by • 0 • written 4.8 years ago by ▴ 60
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 2 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 4 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
0
votes
11
replies
459
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
20 hours ago by Tuck898 • 0
1
vote
9
replies
352
views
UMI-Tools knee-method has great influence on the results of white list
single-cell whitelist UMI RNA UMI-Tools
updated 3 days ago by 19k • written 6 days ago by ★ 1.8k
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 4 days ago by • 0 • written 5.7 years ago by ▴ 30
0
votes
8
replies
412
views
Different output for read length
samtools BAM
3 days ago by marco.barr ▴ 100
2
votes
8
replies
290
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 1 day ago by 161k • written 1 day ago by ▴ 100
3
votes
8
replies
636
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core 16S amplicon dada2 ampliseq
updated 6 days ago by ▴ 410 • written 10 days ago by ▴ 100
3
votes
8
replies
551
views
How to access TCGA samples that were treated with a specific drug?
TCGA RNA-seq
6 days ago by Qroid ▴ 40
0
votes
7
replies
393
views
RNAseq one control two conditions, shared and exclusive genes
conditions RNAseq multiple Rstudio
updated 7 hours ago by ▴ 20 • written 14 days ago by • 0
6
votes
7
replies
318
views
Longest transcript variant per gene
transcript longest variant orthofinder
20 hours ago by sansan_96 ▴ 90
1
vote
7
replies
576
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 3 days ago by 161k • written 5 days ago by • 0
1
vote
7
replies
499
views
Question regarding WGCNA
WGCNA Network-construction
4 days ago by deepak • 0
9
votes
7
replies
7.1k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 2 days ago by • 0 • written 5.7 years ago by ▴ 20
0
votes
7
replies
480
views
Applying the metacell2 algorithm using python
python single-cell scanpy metacell2
updated 4 days ago by ★ 2.0k • written 6 days ago by ▴ 140
3
votes
6
replies
456
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 16 hours ago by ▴ 20 • written 8 days ago by • 0
0
votes
6
replies
2.1k
views
Copy number Variation analysis using conumee
R software error sequencing genome
updated 4 days ago by 142k • written 3.2 years ago by ▴ 10
1
vote
6
replies
695
views
anRichment is missing
WGCNA anRichment
updated 6 days ago by 142k • written 6 months ago by ▴ 180
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 5 days ago by ▴ 10 • written 2.5 years ago by • 0
0
votes
6
replies
356
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf plink bioinformatics genomics
updated 22 hours ago by 161k • written 2 days ago by • 0
4
votes
6
replies
369
views
RNA seq analysis
DESeq RNA-seq
updated 2 hours ago by 4.6k • written 5 days ago by ▴ 10
0
votes
5
replies
295
views
How to convert normalized BigWig file to count matrix?
count-matrix BigWig
12 hours ago by feather-W • 0
0
votes
5
replies
288
views
Too many unpaired forward reads found by Trimmomatic
Trimmomatic
2 hours ago by SilhouetteQ • 0
2
votes
5
replies
494
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 22 hours ago by ▴ 40 • written 10 days ago by ▴ 30
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 5 days ago by ▴ 90 • written 6.4 years ago by ▴ 60
2
votes
5
replies
377
views
Importing a fastq file
Fastq
updated 3 days ago by ▴ 120 • written 4 days ago by • 0
1
vote
5
replies
343
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex bwt
updated 5 days ago by 54k • written 6 days ago by • 0
0
votes
5
replies
299
views
A question about reference genome for creating the consensus sequence
fasta fa cram genome
5 days ago by me • 0
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 5 days ago by • 0 • written 5.1 years ago by ★ 1.8k
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 1 day ago by • 0 • written 6.7 years ago by • 0
5
votes
5
replies
287
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
5 days ago by Chris ▴ 280
1
vote
5
replies
417
views
HCL database download
HCL
updated 5 days ago by 43k • written 9 days ago by ▴ 20
0
votes
5
replies
248
views
Percentage coverage of reference genome by de novo genome
SAMtools BWA alignment ddRAD
updated 5 days ago by 21k • written 5 days ago by • 0
1
vote
4
replies
312
views
Contig assembly task, errors
genetics contig assembly dna bioinformatics
2 days ago by samRayne • 0
0
votes
4
replies
336
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
8 hours ago by beginner123 • 0
3
votes
4
replies
292
views
Truncated metadata file report from ENA Portal API
ena python
2 days ago by Giulia • 0
1
vote
4
replies
394
views
Can I readmap short reads to rDNA references?
rDNA assembly
updated 2 days ago by 142k • written 25 days ago by • 0
3
votes
4
replies
430
views
Design matrix Differential expression analysis
RNA-seq Differential-expression
updated 6 days ago by ★ 7.1k • written 9 days ago by ▴ 40
0
votes
4
replies
395
views
Highest variable features in single cell data
single-cell
6 days ago by carolofharvest ▴ 40
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 2 days ago by • 0 • written 6.4 years ago by ▴ 130
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 5 days ago by • 0 • written 5.5 years ago by 8.4k
2
votes
4
replies
716
views
Count all variants from vcf file
variants vcf Count
updated 6 days ago by 161k • written 20 months ago by • 0
1
vote
4
replies
483
views
cellranger error message
multiplexing cellranger
updated 3 days ago by • 0 • written 3 months ago by ▴ 10
1
vote
4
replies
370
views
Understanding STAR output (Aligned.out.sam file)
STAR paired-end read
5 days ago by heelpPlease • 0
0
votes
4
replies
272
views
Correlation Analysis
statistics methylation NGS expression
2 days ago by Researcher ▴ 30
180 results • Page 1 of 4
Recent Votes
Answer: Practical Haplotype Graph v2 not finding correct paths
A: Looking For A Way To Count Total Length Of Regions Of Bed File
The Biostar Herald for Monday, May 06, 2024
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
A: Find consensus overlap between many bed files
Comment: RNA seq analysis
C: What is the best practice of scRNA workflow for multiple patients and samples us
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Recent Replies
Answer: Splitting Seurat object by sample layers by bk11 ★ 2.4k
You can do the following- Idents(SeuratObj) <- "orig.ident" control_set <- subset(SeuratObj, idents = c("counts.control","data.…
Comment: Galaxy StringTie error by GenoMax 142k
> I have sent a bug report to the Galaxy administrator If you have not done so please post this in Galaxy help forum for directed help: h…
Comment: 44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped by Thind amarinder ▴ 340
Wondering, if it was total RNAseq data? or ployA
Comment: RNA seq analysis by Matthias Zepper 4.6k
It is still obscure to me how many different tissues you would like to include into your comparison and what your intended design is. To …
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Juke34 8.6k
You can get a look here https://www.biostars.org/p/9465973/
Answer: Mouse ribosome sequences in fasta format by GenoMax 142k
A version of the mouse rDNA repeat can be found here: https://www.ncbi.nlm.nih.gov/nuccore/BK000964 Use the dropdown menu at top-left t…
Comment: Kraken2 database by Christopher • 0
Hello, Mathew. Firstly, thank you for answering my question. **Sorry, what analysis are you trying to perform with these databases?** I a…
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by GenoMax 142k
As long as it is the same GIAB sample you could compare your SNP with the SNP's available for the whole genome set.
Comment: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log by yau • 0
Dear Mensur, Thanks so much for your reply!! In my case, I got 1 control(healthy) and 2 disease mouse Single cell RNA-sew data, so I …
Comment: BWA alignment by ATpoint 82k
The relevant code line is precisely the same as in the question.
Answer: imputation through beagle by dthorbur ★ 1.9k
Building a reference panel from the samples you intend to impute seems like a very circular approach. Plus, GBS is a reduced representation…
Answer: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log by Mensur Dlakic ★ 27k
You seem to have too stringent of a p-value cutoff (1e-5). Hopefully you get the concept of how the interplay of `-log10P-value` and `log2F…
Comment: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log by yau • 0
![enter image description here][1] [1]: /media/images/7199a665-b13a-40c8-a065-313cf2b7
Answer: Using samtools with GCS (google cloud storage) on a docker container seems to gi by aw7 ▴ 280
This is a bit late, but the first thing to go is to run `samtools --version` and make sure the docker samtools is configured with the the G…
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools by aw7 ▴ 280
I do not think `samtools fixmate` and `markdup` are going to work on PacBio long reads. `fixmate` is for setting and repairing mate inform…
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