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1,000 results • Page
5 of 20
Sort: Votes
Rank
Views
Votes
Replies
3
votes
6
replies
2.1k
views
Biopython TimeExceptionError how to handle?
biopython
entrez
updated 12 months ago by
Ram
43k • written 6.5 years ago by
Xylanaser
▴ 80
3
votes
3
replies
820
views
When counting ASVs in DADA2, does a hit/count only occur at 100% alignment percent identity?
metagenomics
qiime2
amplicon
16s
dada2
updated 9 months ago by
andres.firrincieli
3.6k • written 9 months ago by
O.rka
▴ 720
3
votes
4
replies
4.1k
views
What are the Pros and Cons of working in Bioinformatics???
career
bio
updated 12 months ago by
Ram
43k • written 6.2 years ago by
scottschu97
▴ 20
3
votes
1
reply
561
views
chromosome location to gene name and aa change
variant-annotation
12 months ago by
Zi
• 0
3
votes
5
replies
1.5k
views
Uniprot API access to download .pdb files
PDB
API
Python
Uniprot
11 months ago by
BioGrad321
• 0
3
votes
9
replies
810
views
Understanding this analysis pipeline
reads
updated 10 months ago by
Ram
43k • written 10 months ago by
artemchuki
• 0
3
votes
1
reply
402
views
FastQC duplicates questions
FastQC
RNA-seq
8 months ago by
Beth
▴ 10
3
votes
3
replies
530
views
How to add value of column to barchart on hover?
R
ggplot
ggplotLy
updated 8 months ago by
Trivas
★ 1.8k • written 8 months ago by
Manuel
▴ 10
3
votes
6
replies
3.3k
views
samtools sort not working when using multiple threads
samtools
bam
updated 11 months ago by
Ram
43k • written 2.3 years ago by
bio_elle
▴ 10
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 27 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
3
votes
5
replies
1.5k
views
Trouble with best practices
samtools
WES
NGS
GATK
updated 12 months ago by
Ram
43k • written 6.3 years ago by
erarroji
• 0
3
votes
2
replies
4.8k
views
How to plot a circular clustered heatmap with dendrogram
circular heatmap
updated 9 months ago by
logbio
▴ 30 • written 4.5 years ago by
The
▴ 180
3
votes
1
reply
572
views
automatic clustering annotation using python
automatic-clustering
single-cell
updated 10 months ago by
Nitin Narwade
★ 1.6k • written 10 months ago by
safeassli
▴ 10
3
votes
5
replies
693
views
ATAC-Seq and featureCounts
ATAC-Seq
featureCounts
updated 4 months ago by
ATpoint
82k • written 4 months ago by
qudrat.nii
▴ 10
3
votes
4
replies
365
views
What should be used as a "baseline" in pooled CRISPR screen?
CRISPR
MAGECK
FACS
9 weeks ago by
Aleksandr
▴ 10
3
votes
2
replies
433
views
Converting STAR Gene-level alignment to TPM expression
RNA-seq
updated 6 months ago by
ATpoint
82k • written 6 months ago by
CTLong
▴ 110
3
votes
6
replies
986
views
Embryo transcriptome
database
transcriptome
SRA
updated 11 months ago by
Basti
★ 2.0k • written 11 months ago by
firefox91
• 0
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 5 weeks ago by
Ram
43k • written 5.6 years ago by
lkianmehr
▴ 100
3
votes
6
replies
3.1k
views
Which of the 4 SureSelect Agilent BED files to use with GATK haplotype caller?
gatk
variant calling
sureselect
updated 9 months ago by
LeandroF.
• 0 • written 4.2 years ago by
curious
▴ 750
3
votes
2
replies
321
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics
Single-Cell
updated 5 weeks ago by
Ram
43k • written 10 weeks ago by
Daddy
▴ 20
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 7 days ago by
chloek88
• 0 • written 5.5 years ago by
Philipp Bayer
8.5k
3
votes
5
replies
1.4k
views
AlphaMissense Plugin VEP
Plugin
VEP
Alphamissense
updated 7 months ago by
Ram
43k • written 7 months ago by
Andrea
▴ 10
3
votes
7
replies
1.1k
views
Use giraffe in vg
giraffe
vg
updated 10 months ago by
Jordan M Eizenga
▴ 460 • written 10 months ago by
Michal
• 0
3
votes
4
replies
1.1k
views
Ballgown DE analysis
R
ballgown
Differential-expression
updated 8 months ago by
Ram
43k • written 2.3 years ago by
iamsmor
• 0
3
votes
1
reply
428
views
Best Tools and Practices for CNV Variant Calling in WES Data
CNV
WES
updated 8 months ago by
Pierre Lindenbaum
161k • written 8 months ago by
Nadav
▴ 20
3
votes
4
replies
485
views
Discrepancy between the downloaded clinvar, dbNSFP and website
dbnsfp
clinvar
updated 5 months ago by
Ram
43k • written 5 months ago by
MAPK2
▴ 40
3
votes
8
replies
1.0k
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST
bowtie2
BWA
alignment
9 months ago by
cheesefish21
▴ 10
3
votes
4
replies
681
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 5 months ago by
Nitin Narwade
★ 1.6k • written 5 months ago by
RNAseqer
▴ 270
3
votes
16
replies
12k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 11 months ago by
Ram
43k • written 5.2 years ago by
Star
▴ 60
3
votes
10
replies
1.3k
views
STAR index not working
STAR
RNA-Seq
7 months ago by
camillab.
▴ 160
3
votes
3
replies
550
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 25 days ago by
swbarnes2
14k • written 26 days ago by
noodle
▴ 580
3
votes
7
replies
392
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
16 days ago by
salias
• 0
3
votes
3
replies
592
views
scrna pipeline
scRNA-seq
updated 10 months ago by
Radu Tanasa
▴ 90 • written 10 months ago by
anasjamshed
▴ 120
3
votes
6
replies
1.0k
views
Screen for transcription factors/genes that maybe the cause of a disease/difference in a phenotype
RNA-seq
ATAC-seq
11 months ago by
Chris
▴ 280
3
votes
3
replies
349
views
learning bioinformatics
course
learning
updated 3 months ago by
Ram
43k • written 3 months ago by
sevda
• 0
3
votes
12
replies
596
views
struggle to get fasta files from ucsc goldenPath
ucsc
getfasta
fasta
6 weeks ago by
Lila M
★ 1.2k
3
votes
5
replies
1.1k
views
Neither pysam nor samtools reading HTTPS-sourced BAM file correctly
bam
pysam
samtools
updated 8 months ago by
Istvan Albert
100k • written 8 months ago by
Alex Reynolds
35k
3
votes
4
replies
747
views
During alignment STAR has stopped at started alignment step
STAR
updated 7 months ago by
Ram
43k • written 9 months ago by
Santhi
• 0
3
votes
4
replies
4.4k
views
Atypical volcano plot RNA-seq
volcano-plot
RNA-seq
deseq2
updated 8 months ago by
Ram
43k • written 5.5 years ago by
Teresa
▴ 20
3
votes
3
replies
358
views
Volcano Plot Output Inquiry: Graphs Facing Down
rstudio
volcano-plot
6 weeks ago by
Pumla
• 0
3
votes
2
replies
1.2k
views
Creating a genotype matrix for BeviMed
snp
genome
Bayesian
updated 11 months ago by
Ram
43k • written 4.3 years ago by
tacrolimus
▴ 140
3
votes
5
replies
1.2k
views
kraken2 bacteria database 250GB+
metagenomics
16s
kraken2
kraken
updated 6 months ago by
GenoMax
142k • written 6 months ago by
10mz1
▴ 10
3
votes
1
reply
587
views
PLINK .ped file issue
plink
updated 6 months ago by
Ram
43k • written 6 months ago by
plinknoob23
• 0
3
votes
6
replies
2.5k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 28 days ago by
Ram
43k • written 22 months ago by
ev97
▴ 20
3
votes
6
replies
871
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 5 months ago by
jv
★ 1.8k • written 5 months ago by
newbee
▴ 40
3
votes
3
replies
2.8k
views
WGCNA Labeled Heatmap
heatmap
wgcna
updated 7 months ago by
Ram
43k • written 2.6 years ago by
Anand
▴ 40
3
votes
3
replies
259
views
Gene Specific coverage from WGS data
WGS
SARS-CoV2
updated 1 day ago by
Ram
43k • written 15 days ago by
Adyasha
• 0
3
votes
14
replies
1.2k
views
How to extract specific region from multiple bam files and merge the outputs into single bam?
bam
rna-seq
updated 6 months ago by
GenoMax
142k • written 6 months ago by
Vasu
▴ 770
3
votes
1
reply
293
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 4 weeks ago by
Ram
43k • written 4 weeks ago by
rj.rezwan
• 0
3
votes
5
replies
944
views
Ensembl site unresponsive in clusterProfiler analyses
parallell
clusterProfiler
R
updated 8 months ago by
manaswwm
▴ 510 • written 8 months ago by
enanoide
• 0
1,000 results • Page
5 of 20
Recent Votes
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
Answer: Cannot install bwa-mem2 via conda
Answer: Sub-sampling a BAM to a fixed number of reads
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Comment: Add stats to boxplot in R
by
Ghada
• 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
▴ 10
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R
by
jared.andrews07
★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
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