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1,000 results • Page
4 of 20
Sort: replies
Rank
Views
Votes
Replies
3
votes
8
replies
567
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
8 days ago by
Qroid
▴ 40
2
votes
8
replies
723
views
TCGA Biospecimens Slides Extraction
tcga
updated 11 weeks ago by
Zhenyu Zhang
★ 1.2k • written 12 weeks ago by
jain72744
▴ 10
3
votes
8
replies
937
views
Can these RNAseq runs be combined?
transcriptomics
replicates
RNAseq
updated 10 months ago by
GenoMax
142k • written 10 months ago by
mdrnao
• 0
1
vote
8
replies
3.5k
views
Best way to address different batches of RNA-seq
sequence
RNA-Seq
RPKM
Fold-Change
batch-effect
updated 27 days ago by
Ram
43k • written 7.1 years ago by
tud55122
▴ 20
5
votes
8
replies
2.5k
views
SV calling using giraffe/vg
vg
Giraffe
calling
structural
variant
updated 9 months ago by
Jordan M Eizenga
▴ 460 • written 16 months ago by
TN
• 0
3
votes
8
replies
2.0k
views
What is the minimum system requement for oxford nanopore read assembly
Assembly
updated 11 months ago by
Ram
43k • written 5.5 years ago by
nagendranp1991
• 0
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
0
votes
8
replies
4.5k
views
Downloading single cell data from NCBI
ncbi
rna-seq
fastq-dump
single-cell
updated 8 months ago by
Ram
43k • written 5.4 years ago by
V
▴ 380
0
votes
8
replies
10.0k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by
Ram
43k • written 6.8 years ago by
himanimalhotra89
• 0
2
votes
8
replies
1.0k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 11 weeks ago by
bharata1803
▴ 560 • written 5 months ago by
LauferVA
4.2k
0
votes
8
replies
1.5k
views
VCF samtools
vcf
samtools
variant-calling
updated 11 months ago by
Ram
43k • written 2.4 years ago by
Lucía
• 0
4
votes
8
replies
1.9k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers
Enhancers
updated 3 months ago by
jared.andrews07
★ 16k • written 3 months ago by
Manhezz
• 0
5
votes
8
replies
1.0k
views
sc-RNA seq pipeline
scRNA-seq
NGS
RNA-Seq
4 months ago by
Researcher
▴ 30
4
votes
8
replies
1.9k
views
Error while running nf-core/rnaseq pipeline
nf-core
RNA-seq
11 months ago by
eesha28112001
• 0
1
vote
8
replies
1.2k
views
Shannon's Entropy by Sliding Window in R
Sequence
Window
R
Entropy
Sliding
updated 11 months ago by
rohitsatyam102
▴ 860 • written 18 months ago by
Alex
• 0
0
votes
8
replies
1.6k
views
Cannot find Output files after applying Markduplicates with picard tools
picard-tools
MarkDuplicates
updated 8 weeks ago by
xiangbinruan
• 0 • written 20 months ago by
Phoebe Magdy
• 0
5
votes
8
replies
2.0k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq
DNA-Seq
contamination
QC
updated 7 months ago by
Jingjingzhang
• 0 • written 3.7 years ago by
from the mountains
▴ 230
1
vote
8
replies
1.0k
views
Reads in IGV are mostly in intron regions
Patchseq
RNA-seq
10 months ago by
Kai_Qi
▴ 130
5
votes
8
replies
650
views
Multiple threads on ubuntu server
Ubuntu
updated 3 months ago by
colindaven
6.4k • written 3 months ago by
oghzzang
▴ 50
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 5 weeks ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 11 months ago by
Ram
43k • written 4.0 years ago by
kand3e
▴ 60
1
vote
8
replies
1.1k
views
How does one access TCGA controlled data in AWS S3?
tcga
aws
updated 7 months ago by
Zhenyu Zhang
★ 1.2k • written 7 months ago by
Cmouli
▴ 10
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core
metaboigniter
nextflow
updated 8 months ago by
Phil Ewels
★ 1.4k • written 8 months ago by
eesha28112001
• 0
1
vote
8
replies
1.1k
views
Mitochondrial genes - TPM calculation bulk RNA-Seq
TPM
RNA-Seq
mtDNA
6 months ago by
nick_b55
▴ 10
1
vote
8
replies
531
views
Downsampling fastq file
downsample
fastq
14 days ago by
marco.barr
▴ 110
1
vote
8
replies
869
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq
deseq2
5 months ago by
pingu77
▴ 20
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan
SNP
updated 10 months ago by
Ram
43k • written 9.6 years ago by
zhaojianli198322
• 0
3
votes
8
replies
651
views
Huge decrease of BUS records using bustools
single-cell
bustools
10X
11 weeks ago by
julien.wollbrett
• 0
2
votes
7
replies
1.1k
views
error: BLAST database name is missing. Please edit provean.sh file to add the name.
provean
error
updated 8 months ago by
GenoMax
142k • written 8 months ago by
elham
• 0
3
votes
7
replies
1.4k
views
Find 3'UTRs for species
Assembly
alignment
updated 11 months ago by
Ram
43k • written 4.7 years ago by
Palgrave
▴ 110
4
votes
7
replies
820
views
Help with weighted nearest neighbor analysis
seurat
single-cell
8 months ago by
Chris
▴ 280
0
votes
7
replies
617
views
Trying to extract .cram file read sequences into array
CRAM
pysam
reads
samtools
11 weeks ago by
sacryt
• 0
1
vote
7
replies
844
views
alignment tool for big data
sequence
updated 10 months ago by
Ram
43k • written 4.6 years ago by
gbahramali
▴ 20
1
vote
7
replies
881
views
Ribosomal cluster
seurat
single-cell
7 months ago by
Chris
▴ 280
0
votes
7
replies
2.0k
views
CIBERSORTx error: 'x' must be an array of at least two dimensions
matrix
CIBERSORTx
signature
updated 6 months ago by
kkj3083
• 0 • written 22 months ago by
Jie
• 0
1
vote
7
replies
1.3k
views
For loop STAR not working
RNA-Seq
STAR
updated 10 months ago by
Ram
43k • written 2.9 years ago by
vinishavvenugopal
▴ 30
0
votes
7
replies
4.5k
views
align_and_estimate_abundance.pl (rsem-parse-alignments: /lib64/libz.so.1: version `ZLIB_1.2.3.3' not found (required by rsem-parse-alignments))
RNA-Seq
alignment
software-error
next-gen
sequence
updated 5 months ago by
Ram
43k • written 6.0 years ago by
nasreenbano91
• 0
0
votes
7
replies
2.7k
views
How to perform gene annotation in kallisto?
Gene
kallisto
annotation
updated 8 months ago by
호성
• 0 • written 2.7 years ago by
synat.keam
▴ 100
7
votes
7
replies
5.0k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines
DESeq2
time-series
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.3 years ago by
stu111538
▴ 80
2
votes
7
replies
1.3k
views
Weirdness in annotation (missing allele frequencies)
allele-frequency
gnomad
annovar
updated 7 months ago by
Ram
43k • written 7 months ago by
Can Abdullah
• 0
5
votes
7
replies
982
views
Salmon index not progressing
salmon
updated 7 months ago by
Michael
54k • written 7 months ago by
camillab.
▴ 160
1
vote
7
replies
914
views
help with weird PCA? (vcfR)
vcftools
vcfR
R
6 months ago by
MaeBH
• 0
0
votes
7
replies
1.3k
views
FACS (Fluorescence-activated cell sorting NOT cyTOF),Automating the removal of dead and duplicated cells
FACS
updated 7 months ago by
rfran010
▴ 900 • written 8 months ago by
ccbb7aab4
▴ 20
8
votes
7
replies
596
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 3 months ago by
Ram
43k • written 3 months ago by
synat.keam
▴ 100
0
votes
7
replies
1.6k
views
Comparing the GVF file & VCF file
gvf
dna
vcf
ensembl
ngs
updated 6 months ago by
mickeykuo129
• 0 • written 16 months ago by
Alireza
▴ 30
0
votes
7
replies
736
views
error MarkerScanner.pl
amphora2
updated 5 months ago by
Ram
43k • written 5 months ago by
Kárita
• 0
4
votes
7
replies
436
views
RNA seq analysis
DESeq
RNA-seq
2 hours ago by
Jacek
▴ 10
3
votes
7
replies
6.4k
views
Human reference files in HG38 GATK resource bundle
VCF
updated 11 months ago by
DareDevil
★ 4.3k • written 6.3 years ago by
win
▴ 980
1
vote
7
replies
3.1k
views
RGT TypeError: unsupported operand type(s) for +: 'NoneType' and 'int'
RGT
TF-footprinting
ATAC-seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
7
replies
1.6k
views
Accuracy of Methods for Gene Variant Detection and Quantification: Kallisto Pseudoalignment vs. STAR Alignment
kallisto
STAR
RNA-seq
Transcript_variants
12 months ago by
sohail.mbio
• 0
1,000 results • Page
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Recent Votes
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
What is Deepvariant default filtering values ?
Answer: Filtering Multi-sample VCF file for all except one Genotype
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
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Answer: Duplicated reads (IDs) from nanopore sequencing
by
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▴ 110
Hi, I'm also working with ONT data and with dorado. From experience I tell you that some versions of MInKNOW have bad management of fast5 f…
Comment: Problem with Calling Variants from RNA-Seq data
by
Esraa
• 0
Yes, i specifically ran the RNA-seq best practices, and no i have not taken RNA editing into account considering this is not mentioned in t…
Comment: Problem with Calling Variants from RNA-Seq data
by
i.sudbery
19k
Have you accounted for A>I RNA editing?
Comment: Problem with Calling Variants from RNA-Seq data
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Thank you so much Matthias this is really helpful, I got insight from this. Have a nice day
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> Is this a statistically valid approach to compare the impact of any bacterial exposure and genotype? At a glance, it seems fine to me…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Filtering VCF files based on VAF giving incorrect results
by
Pierre Lindenbaum
161k
using vcfilterjdk: https://jvarkit.readthedocs.io/en/latest/VcfFilterJdk/ java -jar ${JVARKIT_DIST}/jvarkit.jar vcffilterjdk …
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I have one more question please. When reading the h5ad file at the very beginning, do I need to perform the usual scanpy normalization step…
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Thank you! This was going to be my next option - to simply use the Read_1 libraries for all samples. Can I ask about the second option you…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
schmince
• 0
Thanks, that was exactly what i needed
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
Esraa
• 0
Thank you! I will try searching for this more and see if it would fit my analysis purposes.
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
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Esraa
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Thank you so much for answering! I actually found some studies doing it the way you mentioned. I ran the GATK best practices pipeline on t…
Comment: BWA alignment
by
a.alnawfal.1992
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that's great, but i believe the issue is related to stdin rather than index
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