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707 results • Page
1 of 15
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Votes
Replies
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
26 days ago by
Kevin Blighe
88k
29
votes
28
replies
35k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 19 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 21 days ago by
i.sudbery
19k • written 24 days ago by
noodle
▴ 580
9
votes
23
replies
9.9k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
10 days ago by
vytarasov
▴ 180
13
votes
17
replies
6.1k
views
9 follow
Blastn, need help to increase speed
RNA-Seq
blastn
blast+
updated 1 day ago by
m13113153781
• 0 • written 3.2 years ago by
chiachoong_leong93
▴ 20
7
votes
16
replies
986
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
22 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 14 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
1
vote
16
replies
783
views
Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NULL > pointer.
blast
ncbi
updated 3 days ago by
GenoMax
142k • written 6 days ago by
hophuquy0944
• 0
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 25 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 17 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
19
votes
15
replies
2.3k
views
Forum:
What is the amount of sequencing data produced annually?
data
research
sequencing
updated 10 hours ago by
Mohamed
• 0 • written 8 months ago by
vincenthus
▴ 70
1
vote
14
replies
2.5k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 18 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 1 day ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
10
votes
14
replies
830
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 14 days ago by
GenoMax
142k • written 20 days ago by
nicole.kavanagh
• 0
2
votes
14
replies
3.0k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 7 days ago by
Anitha
• 0 • written 4.9 years ago by
ww22runner
▴ 60
13
votes
14
replies
1.0k
views
High Malat-1 expression in single cell data
single-cell
updated 13 days ago by
t.montserrat.ayuso
▴ 40 • written 22 days ago by
carolofharvest
▴ 40
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 11 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 27 days ago by
drstalinantony28
• 0 • written 2.3 years ago by
ymj
▴ 10
38
votes
12
replies
31k
views
9 follow
How to systematically check if a bam file is truncated
Exomeseq
updated 4 days 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 18 days ago by
rsieber
▴ 10 • written 3.2 years ago by
Kumar
▴ 120
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 12 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
2
votes
11
replies
1.0k
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 22 days ago by
jkbonfield
★ 1.2k • written 4 weeks ago by
me
• 0
0
votes
11
replies
576
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
9 days ago by
Tuck898
• 0
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 28 days ago by
Ram
44k • written 14.6 years ago by
Istvan Albert
100k
4
votes
11
replies
911
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 27 days ago by
LauferVA
4.2k • written 28 days ago by
dominickd
• 0
2
votes
11
replies
765
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
4 days ago by
egascon
• 0
1
vote
11
replies
5.6k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 15 days ago by
guanghao
• 0 • written 6.2 years ago by
vivekruhela
▴ 20
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 25 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
0
votes
11
replies
736
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
25 days ago by
atowns21
• 0
1
vote
10
replies
1.1k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
27 days ago by
DKA
▴ 40
40
votes
10
replies
43k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 22 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
4
votes
10
replies
848
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 13 hours ago by
Alex Reynolds
35k • written 25 days ago by
J
▴ 10
2
votes
10
replies
1.1k
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 1 day ago by
Ram
44k • written 5 months ago by
LauferVA
4.2k
17
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 580
1
vote
10
replies
910
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 15 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
0
votes
10
replies
655
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 21 days ago by
i.sudbery
19k • written 29 days ago by
Patadu94
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
22 days ago by
anna
▴ 20
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 22 days ago by
Ram
44k • written 9 months ago by
Gio
• 0
0
votes
9
replies
618
views
Using VEP annotation output as the input for a second VEP annotation
Annotation
VEP
VCF
5 days ago by
Arton
▴ 10
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 18 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
3
votes
9
replies
647
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 27 days ago by
Istvan Albert
100k • written 29 days ago by
Κοσμάς
• 0
4
votes
9
replies
635
views
In one PCA plot, can I calculate the percentage of different factors that contribute to the PCA?
PCA
R
VARIANCE
updated 11 hours ago by
marco.barr
▴ 130 • written 6 days ago by
diqixiaoyaoer
▴ 20
0
votes
9
replies
388
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
5 days ago by
njornet
▴ 20
1
vote
9
replies
462
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 11 days ago by
i.sudbery
19k • written 14 days ago by
Assa Yeroslaviz
★ 1.8k
2
votes
9
replies
959
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 27 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
0
votes
9
replies
1.5k
views
kinannote software installation problems
kinannote
updated 13 days ago by
Emanoelle
• 0 • written 5.8 years ago by
Elizabeth
▴ 30
2
votes
9
replies
767
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 6 days ago by
Pierre Lindenbaum
161k • written 14 days ago by
schmince
• 0
0
votes
9
replies
672
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 6 days ago by
Wayne
★ 2.0k • written 15 days ago by
JACKY
▴ 140
4
votes
9
replies
510
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch
alignment
4 days ago by
Gabriel R.
★ 2.9k
0
votes
8
replies
504
views
Different output for read length
samtools
BAM
12 days ago by
marco.barr
▴ 130
707 results • Page
1 of 15
Recent Votes
Comment: Super ehancers
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Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
Answer: Differential Expression with limma: Contrast and Design Matrix, combinatorial ap
Answer: tensorQTL interaction issue
Answer: converting transcript IDs (Ensembl) to gene symbols in R
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Comment: Where are the illumina adapters on Trimmomatic take from?
by
GenoMax
142k
Illumina indexed adapters share a core sequence at the beginning which is what is indicated in your link. Trimming programs will remove seq…
Comment: Allele count of 2 for homoplasmic MT variants in VCF
by
Ram
44k
Please stop using `bioinformatics` as a tag unless your post is about the field of bioinformatics itself.
Comment: Multiplexing for pooled CRISPR screen sequencing
by
GenoMax
142k
> If we switch to pair-end sequencing with dual-index barcode You can use dual-indexing with single end reads. You don't need to do paired…
Comment: Super ehancers
by
jared.andrews07
★ 17k
That is not valid GFF format, so that is probably going to be problematic. See the [GFF spec](https://github.com/The-Sequence-Ontology/Spec…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
finch
• 0
Hey! I had this issue and I think I can help- could you take a screenshot of the .txt file opened in the notepad?
Answer: Is it possible to run CibersortX with a very small number of samples?
by
finch
• 0
Hi! I had a very similar issue and it's likely not at all related to your number of samples but to the format of your mixture file! Ciberso…
Comment: How can we convert a vcf to fasta, so that I can blast some genes against that w
by
Ram
44k
You cannot *convert* a VCF to a FASTA as they have vastly different information content. Please explain your process - what exactly do you …
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Shukai
• 0
Thank you Ram for the comments! Noted for future posts.
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
I am looking for diagrams, and step-by-step instructions of how to build my pipelines. I think the github is only helpful if you are a wdl…
Comment: Where to find old version of GATK best practice
by
Zhenyu Zhang
★ 1.2k
oh, this is helpful. Thanks.
Comment: Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis o
by
Ram
44k
1. You can edit your post and add relevant details. There is no need to add separate comments with relevant details especially when it's no…
Answer: Functional enrichment analysis for unique gene IDs
by
geneontologyhelp
▴ 400
If you are looking at producing GO annotations, we currently only recommend InterProScan, and basically only for novel organisms or where t…
Answer: Question about samtools view flags (paired reads vs. properly paired reads)
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paired reads = the experiment was a paired end assay: each fragment was sequenced on 5' and 3', two FASTQ files are generated by the seque…
Answer: z-score of gene set
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4.6k
The z-score is a measure of how many standard deviations a particular data point is from the mean of a distribution. A positive z-score ind…
Answer: converting transcript IDs (Ensembl) to gene symbols in R
by
bk11
★ 2.5k
You can do as following: library(biomaRt) # Set up the Ensembl BioMart connection ensembl <- useEnsembl(biomart = "genes",…
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