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11
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DEgs RNAseq
RNAseq
1 hour ago by Juan • 0
0
votes
2
replies
196
views
Counting intronic reads in bulk RNA-seq
rna-seq
updated 2 hours ago by 13k • written 1 day ago by ▴ 300
0
votes
2
replies
157
views
Single cell chemistry
cell single chemistry
updated 3 hours ago by 13k • written 16 hours ago by • 0
0
votes
0
replies
32
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS download data
3 hours ago by Vincent Laufer ★ 2.8k
0
votes
6
replies
306
views
Why are some WES VCFs larger than others?
WES sequencing genomics NGS exome
updated 7 hours ago by ★ 2.8k • written 1 day ago by ▴ 80
0
votes
4
replies
177
views
SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC.
snakemake
5 hours ago by Dhatri Badri • 0
0
votes
0
replies
60
views
problem of Global Biobank Meta-analysis Initiative
GWAS
10 hours ago by 1362321710 • 0
743
votes
162
replies
113k
views
101 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 4 weeks ago by 1.8k • written 6.5 years ago by 98k
0
votes
1
reply
95
views
DownsampleSam
picard DownsampleSam
updated 10 hours ago by 154k • written 11 hours ago by • 0
0
votes
2
replies
158
views
ABySS genome assembler
ABySS genome k-mers assembly
11 hours ago by npavliukovec • 0
0
votes
0
replies
79
views
Error while running Megahit
Megahit
updated 14 hours ago by 129k • written 19 hours ago by • 0
0
votes
1
reply
114
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA Expression mRNA
updated 4 hours ago by ★ 2.8k • written 23 hours ago by ▴ 30
1
vote
5
replies
262
views
Cutadapt error: too many parameters.
cutadapt parallel bash
updated 1 day ago by 129k • written 1 day ago by • 0
0
votes
0
replies
111
views
corresponding clinical data from TCGA database of PSI values for CCA AS events in spliceseq database
TCGA
1 day ago by dima • 0
1
vote
0
replies
166
views
How to assess which cell population is most affected by treatmant in single cell rna seq data?
transcriptomics single-cell RNA DEG
1 day ago by abbas89 ▴ 10
0
votes
3
replies
288
views
metric informing about the similarity of gene lists in OrderedList
orderedlist
updated 1 day ago by ★ 2.8k • written 2 days ago by • 0
18
votes
6
replies
6.4k
views
VCF header line counting
vcf header
updated 1 day ago by ▴ 530 • written 8.3 years ago by ▴ 40
0
votes
1
reply
132
views
How extract specific SNP position from the bed file-Bedtools
bedtools for Help
updated 1 day ago by 129k • written 1 day ago by • 0
0
votes
0
replies
369
views
Can I send my PyMol results to a web-page as a result for a submitted query? If not, how can I get a 3d render of a protein as a result for a user su…
protein-structure pymol protein pdb python
1 day ago by Aatif Hashmi • 0
2
votes
5
replies
366
views
Design matrix to remove technical replicate effect
edgeR
1 day ago by ARD ▴ 10
0
votes
1
reply
214
views
Deferentially expressed gene with high log2foldchange by DESeq2; but not meaningful at the individual level
DESeq2 RNA-seq DGEA
updated 1 day ago by ★ 2.8k • written 1 day ago by ▴ 10
1
vote
2
replies
159
views
Abyss taking a Long time to run
abyss assembly genome fastq
1 day ago by Maliha ▴ 20
0
votes
2
replies
186
views
Import or read Snapgene .dna files into R
R .dna snapgene
1 day ago by eggrandio ▴ 40
2
votes
2
replies
180
views
Segmentation fault Biopython pairwise alignment
biopython alignment
updated 1 day ago by 98k • written 1 day ago by ▴ 20
0
votes
3
replies
273
views
Biological replicates in RNA-seq
RNA-seq biological-replicates
updated 1 day ago by ★ 1.8k • written 2 days ago by • 0
0
votes
0
replies
87
views
BEAST Divergence time Analysis
time BEAST BEAUti divergence
1 day ago by ahmadjoyyia ▴ 10
0
votes
0
replies
102
views
Differential Gene Expression analysis in heterogeneous tissues
RNA-seq deseq2
updated 1 day ago by 39k • written 1 day ago by ▴ 70
2
votes
2
replies
239
views
Plotting heat map with significance based on multiple columns
R Python Heatmap
updated 1 day ago by 3.7k • written 2 days ago by ▴ 50
1
vote
1
reply
135
views
Issue with MiSeq Demultiplexing: Unexpected Ns in I5_Index
MiSeq Demultiplexing Sequencing
updated 1 day ago by 129k • written 1 day ago by • 0
4
votes
5
replies
436
views
bitr() doesn't recognize the keys I've entered as valid gene symbols for my organism's database ('SYMBOL').
pathway-analysis clusterProfiler
1 day ago by Medeea • 0
3
votes
2
replies
237
views
vg: Mapping fewer reads to a genome graph than a linear reference
giraffe mapping pangenome vg
updated 13 hours ago by ▴ 470 • written 2 days ago by ▴ 20
0
votes
1
reply
151
views
Variant Annotation
Variant-Annotation VCF R
updated 1 day ago by 39k • written 1 day ago by • 0
0
votes
0
replies
115
views
News: course - Advanced Python programming
Programming DeepLearning Python MachineLearning
1 day ago by carlopecoraro2 ★ 2.3k
0
votes
1
reply
154
views
too many zeros in 16S rRNA amplicon sequencing data
16S rRNA
updated 9 hours ago by 3.3k • written 1 day ago by ▴ 180
0
votes
0
replies
131
views
Job: Looking for a internship or master's course in Bioinformatics
masters internship career
updated 1 day ago by 39k • written 1 day ago by • 0
0
votes
1
reply
172
views
Seurat 'DoHeatmap()' hierarchical clustering
DoHeatmap Seurat clustering
updated 1 day ago by ▴ 940 • written 2 days ago by • 0
3
votes
2
replies
230
views
Bioinformatics in drug designing
pharmaceutical
1 day ago by nishimalhotra2612 ▴ 40
0
votes
1
reply
139
views
Finding Kinetic Parameters from Western Blot images
image-processing western-blot
updated 1 day ago by 39k • written 1 day ago by • 0
3
votes
1
reply
3.2k
views
How To Interpret The Numbers In The Cnvnator Genotype Output
genotyping
updated 1 day ago by • 0 • written 10.4 years ago by ▴ 150
0
votes
0
replies
118
views
Chipseq data peak calling issue
Bioinformatics sequencing chipseq RNA data
1 day ago by Adyasha • 0
0
votes
2
replies
241
views
NanoSim Error "Please specify the training reads and its reference genome!"
NanoSim RNA-seq LongRead
1 day ago by akainth • 0
3
votes
4
replies
289
views
rose identifies super enhancers, how to output PDF files
PDF rose
updated 2 days ago by 39k • written 2 days ago by • 0
0
votes
0
replies
120
views
Assigned taxonomy after dada2 only "NAs" or "Mitochondria"
16S dada2 DECIPHER ITS taxonomy
2 days ago by mattze731 • 0
0
votes
0
replies
114
views
I want to set the null hypothesis for the test of genetic correlation to rg=1.
correlation LDSC genetic
2 days ago by Apprentice ▴ 130
3
votes
2
replies
199
views
How to download iGenomes from S3
iGenome
2 days ago by Chris ▴ 100
2
votes
3
replies
233
views
sambamba-depth: All files must be coordinate-sorted error?
read linux sambamba
updated 2 days ago by 154k • written 2 days ago by ▴ 10
2
votes
6
replies
608
views
Prokka installation - compilation aborted
database Prokka compilation indexing
2 days ago by eimanpharmacist ▴ 20
0
votes
2
replies
233
views
About inconsistent cell counts per samples obtained in small nuclear RNAseq data.
Seurat QC Single-Cell
1 day ago by bk11 ▴ 60
0
votes
3
replies
691
views
samtools installed but error message: Library not loaded: @rpath/libcrypto.1.0.0.dylib
Monterey samtools macOS
updated 2 days ago by 129k • written 13 months ago by • 0
4
votes
6
replies
603
views
samtools install error
samtools
updated 2 days ago by • 0 • written 4 weeks ago by ▴ 10
1,000 results • Page 1 of 20
Recent Votes
Answer: IGV displays genomic coordinates in a 1-based system or 0-based?
RNAseq expression data log2 transformed has negative values.
Samtools: "Too Many Open Files"
Filtering bad quality probes in illumina microarray data
gene filtering for agilent microarray using Limma
A: Identification Of Significant Differences Between Phylogentic Trees Using Distan
A: How to filter vcf file on minimum genotype depth and quality for each sample
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Recent Replies
Answer: Counting intronic reads in bulk RNA-seq by swbarnes2 13k
Are you sure this is appropriate for bulk RNASeq? I thought intronic reads for single cell were only counted in nuclear preps.
Answer: Single cell chemistry by swbarnes2 13k
Are you sure these samples are 10x? How likey is it that the sequencing group messed up and ran the samples wrongly?
Comment: How to deal with duplicated gene IDs in TCGA RNA expression data? by Vincent Laufer ★ 2.8k
are they distinct transcript IDs but the same gene ID? can you provide any additional context?
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Dhatri Badri • 0
that didn't work either
Answer: Why are some WES VCFs larger than others? by Vincent Laufer ★ 2.8k
Hi @kermit and prash (and others)! Nice discussion. I wanted to offer some **biological rationales** in addition to the technical reasons …
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by WouterDeCoster 47k
There is no `:` after `rule fastqc`
Comment: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Dhatri Badri • 0
sorry that was a typo while i was copying my code! I still get the same error
Comment: too many zeros in 16S rRNA amplicon sequencing data by andres.firrincieli 3.3k
You have too many ASV (40k) and I think this is a problem related to the denoising (DADA2) of NovaSeq 6000 sequencing data. Maybe this post…
Answer: SyntaxError (Perhaps you forgot a comma?) in snakefile when running FastQC. by Pierre Lindenbaum 154k
> fastq.gz". what is the dot after `fastq.gz" ` ?
Comment: DownsampleSam by Pierre Lindenbaum 154k
1) I think this is just a warning 2) there must be another error displayed 3) look at samtools view --subsample 4) don't use loops but use…
Comment: ABySS genome assembler by npavliukovec • 0
Hello, yes, I tried it, but I have to do my home work on university's remote computer, unfortunatelly I go an error, when I try to use abys…
Comment: desgin a primer for CDS by yuxiang • 0
how can you know the primer is not bind to other gene site? how can you desgin an experiment? I use the FISH to identify the gene, how abo…
Comment: desgin a primer for CDS by yuxiang • 0
sorry for my late reply, I am a student, my profossor ask me to dsgin a primer for the specific cDNA, I have solved now, thanks for your re…
Comment: vg: Mapping fewer reads to a genome graph than a linear reference by samuel.a.odonnell ▴ 470
In this case filtering for quality might help correct for this overattributing feature?
Comment: ABySS genome assembler by GenoMax 129k
Did you see this guidance from ABySS manual: https://github.com/bcgsc/abyss#optimizing-the-parameters-k-and-kc
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