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737 results • Page
1 of 15
Sort: replies
Rank
Views
Votes
Replies
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
23 days ago by
Kevin Blighe
88k
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 15 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
38
votes
24
replies
2.3k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 18 days ago by
i.sudbery
19k • written 20 days ago by
noodle
▴ 580
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
7 days ago by
vytarasov
▴ 180
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 29 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
7
votes
16
replies
955
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
19 days ago by
Ruqaiya
• 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 11 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
34
votes
16
replies
21k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 29 days ago by
Hagen
▴ 10 • written 10.3 years ago by
filipzembol
▴ 180
1
vote
16
replies
680
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 22 minutes ago by
GenoMax
142k • written 2 days ago by
hophuquy0944
• 0
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 21 days ago by
bk11
★ 2.5k • written 10 weeks ago by
Sofia
• 0
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 14 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
13
votes
14
replies
949
views
High Malat-1 expression in single cell data
single-cell
updated 10 days ago by
t.montserrat.ayuso
▴ 40 • written 19 days ago by
carolofharvest
▴ 40
10
votes
14
replies
790
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 11 days ago by
GenoMax
142k • written 16 days ago by
nicole.kavanagh
• 0
1
vote
14
replies
2.5k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 15 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 4 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 24 days ago by
drstalinantony28
• 0 • written 2.3 years ago by
ymj
▴ 10
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 7 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
5
votes
13
replies
2.0k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 28 days ago by
ATpoint
82k • written 29 days ago by
BioinfGuru
★ 1.7k
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 23 hours ago by
alanh
▴ 170 • written 7.1 years ago by
jonessara770
▴ 240
16
votes
12
replies
7.5k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 15 days ago by
rsieber
▴ 10 • written 3.2 years ago by
Kumar
▴ 120
11
votes
12
replies
1.2k
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 29 days ago by
Ram
43k • written 29 days ago by
iamsmor
• 0
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 29 days ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 9 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
2
votes
11
replies
677
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
1 day ago by
egascon
• 0
0
votes
11
replies
716
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
22 days ago by
atowns21
• 0
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 22 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
0
votes
11
replies
545
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
5 days ago by
Tuck898
• 0
4
votes
11
replies
888
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 24 days ago by
LauferVA
4.2k • written 25 days ago by
dominickd
• 0
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 19 days ago by
jkbonfield
★ 1.2k • written 4 weeks ago by
me
• 0
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 24 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
1
vote
11
replies
5.6k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 12 days ago by
guanghao
• 0 • written 6.2 years ago by
vivekruhela
▴ 20
9
votes
10
replies
7.0k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 29 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
0
votes
10
replies
641
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 18 days ago by
i.sudbery
19k • written 26 days ago by
Patadu94
• 0
1
vote
10
replies
892
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 12 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 18 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
23 days ago by
DKA
▴ 40
3
votes
9
replies
623
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 24 days ago by
Istvan Albert
100k • written 25 days ago by
Κοσμάς
• 0
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 19 days ago by
Ram
43k • written 9 months ago by
Gio
• 0
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by
dvelmeshev
• 0
0
votes
9
replies
610
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 3 days ago by
Wayne
★ 2.0k • written 11 days ago by
JACKY
▴ 140
0
votes
9
replies
352
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
2 days ago by
njornet
▴ 20
1
vote
9
replies
403
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 8 days ago by
i.sudbery
19k • written 11 days ago by
Assa Yeroslaviz
★ 1.8k
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
18 days ago by
anna
▴ 20
4
votes
9
replies
427
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
1 day ago by
Gabriel R.
★ 2.9k
2
votes
9
replies
942
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 24 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
2
votes
9
replies
707
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 3 days ago by
Pierre Lindenbaum
161k • written 10 days ago by
schmince
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 9 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
4
votes
9
replies
2.2k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 15 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
0
votes
9
replies
602
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
2 days ago by
Arton
▴ 10
3
votes
8
replies
690
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 11 days ago by
Chris Dean
▴ 410 • written 15 days ago by
sovrappensiero
▴ 100
737 results • Page
1 of 15
Recent Votes
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
C: How can I perform Differential expression analysis with just one control and one
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Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the bug by removing nucmer threading flag "**-t**" from line#16 of psvcp_v1.01-main script "**Refgenome_update_by_quest.sh"**.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
▴ 10
Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
by
swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
Comment: GG Sankey plot
by
LauferVA
4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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