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187 results • Page
4 of 4
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Views
Votes
Replies
0
votes
0
replies
88
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 6 days ago by
Ram
43k • written 6 days ago by
SSSJec
• 0
0
votes
6
replies
334
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
5 days ago by
Sd
• 0
0
votes
2
replies
183
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
6 days ago by
sainavyav22
• 0
0
votes
1
reply
148
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 6 days ago by
Ram
43k • written 6 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
339
views
Error in cnetplot enrichplot package
R
updated 6 days ago by
Ram
43k • written 6 days ago by
Farhad
• 0
3
votes
9
replies
468
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 5 days ago by
Istvan Albert
100k • written 6 days ago by
Κοσμάς
• 0
0
votes
0
replies
110
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 6 days ago by
Ram
43k • written 6 days ago by
maxime.policarpo
▴ 200
3
votes
3
replies
205
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 6 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
c_u
▴ 520
0
votes
0
replies
93
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 6 days ago by
Ram
43k • written 6 days ago by
sansan_96
▴ 80
0
votes
0
replies
99
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 6 days ago by
Ram
43k • written 6 days ago by
Amélie
• 0
0
votes
0
replies
202
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 6 days ago by
Ram
43k • written 6 days ago by
Oak
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 6 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
2
votes
3
replies
213
views
from row count to tpm
tpm
row-count
normalization
6 days ago by
michelafrancesconi9
▴ 20
1
vote
7
replies
339
views
Downsampling fastq file
downsample
fastq
updated 1 hour ago by
Ram
43k • written 7 days ago by
marco.barr
▴ 80
2
votes
3
replies
336
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 3 days ago by
dsull
★ 5.9k • written 19 days ago by
javanokendo
▴ 60
0
votes
7
replies
340
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
GenoMax
141k • written 7 days ago by
Patadu94
• 0
0
votes
0
replies
80
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
6 days ago by
alifafiq1
• 0
76
votes
72
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
4 days ago by
Kevin Blighe
87k
2
votes
4
replies
295
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
5 days ago by
samuelkalandarov2002
▴ 10
2
votes
4
replies
323
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
5 days ago by
HyperEvo
• 0
1
vote
5
replies
356
views
DYH17 Structure Prediction
BLAST
Protein-Structure-Prediction
6 days ago by
anasjamshed
▴ 120
2
votes
11
replies
803
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 6 hours ago by
jkbonfield
★ 1.2k • written 12 days ago by
me
• 0
0
votes
6
replies
445
views
Use of Kraken output for functional analysis
metagenomics
kraken
shotgun
updated 5 days ago by
gv
• 0 • written 28 days ago by
Srinka
▴ 20
4
votes
2
replies
381
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 3 days ago by
shalespringer
• 0 • written 11 weeks ago by
Phenylananin
▴ 20
0
votes
2
replies
590
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 4 days ago by
Dateline
• 0 • written 21 months ago by
JZX
• 0
1
vote
5
replies
605
views
Cell barcode whitelists for DNBelab C Series High-throughput Single-cell RNA Series Library Preparation Set?
cell-barcode
MGI
DNBelab
single-cell
updated 5 days ago by
atowns21
• 0 • written 3 months ago by
benjamin.pyenson
• 0
0
votes
3
replies
284
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 1 hour ago by
Ram
43k • written 4 months ago by
Fadi
• 0
1
vote
4
replies
434
views
GTF file for Rhinolophus sinicus
Rhinolophus-sinicus
GTF
updated 5 days ago by
atowns21
• 0 • written 5 months ago by
ara
• 0
0
votes
0
replies
276
views
Choice of relatedness cutoff for GWAS of a large cohort (>100K samples)
relatedness
IBD
GWAS
updated 6 days ago by
Ram
43k • written 14 months ago by
Oak
▴ 10
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 4 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
2
votes
3
replies
2.5k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel
gatk
calling
snp
variant
updated 1 day ago by
zihanss
• 0 • written 23 months ago by
Vitor1
▴ 120
2
votes
6
replies
3.7k
views
Treatment VS Control in Single Cell RNAseq analysis
Single Cell
RNAseq
DE Analysis
Treatment
Control
updated 3 days ago by
ATpoint
82k • written 3.9 years ago by
grayapply2009
▴ 280
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 4 hours ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
7
votes
7
replies
5.9k
views
6 follow
How to know synonymous and non-synonymous SNPs from transcriptome sequencing
RNA-Seq
SNP
updated 3 days ago by
rohitsatyam102
▴ 850 • written 6.1 years ago by
smallfish
▴ 10
25
votes
11
replies
3.7k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 5 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
10
votes
6
replies
9.9k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 3 days ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
14
votes
2
replies
7.0k
views
Trouble with Pilon installation
polishing
pilon
installation
updated 4 days ago by
Lissa Cruz Saavedra
• 0 • written 7.3 years ago by
Rox
★ 1.4k
187 results • Page
4 of 4
Recent Votes
Answer: Mapping ortholog human and mouse transcript
C: Kallisto missing Bootstrap
Answer: Very low RNA splicing rate for pulmonary AT2 cells
Answer: what is the purpose of indexing the reference genome (Kallisto)
The Biostar Herald for Monday, April 29, 2024
The Biostar Herald for Monday, April 29, 2024
Comment: NGS forensics: how to know if data is fabricated
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Recent Awards •
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e.r.zakiev
▴ 200
Popular Question
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Bine
▴ 60
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★ 4.2k
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Recent Replies
Comment: Genbank File Format
by
Mensur Dlakic
★ 27k
I think this is a question for CLC support. It should be trivial for them to combine these fields into one. In other words, you need a bett…
Answer: Programmatically retrieving positions of protein active site residues
by
Mensur Dlakic
★ 27k
Although this probably doesn't qualify as `programmatically retrieving positions`, you can always do it by sequence alignments. This can be…
Answer: metagenomic virome quality assessment
by
Mensur Dlakic
★ 27k
The error message points to a problem with `prodigal-gv`. What happens when you type `prodigal-gv` on the command line? It is never a go…
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★ 2.0k
"I have seen other similar posts but a lot of the tools and websites suggested are down." Please show & share your research as part of you…
Comment: Software to separate reads from different individuals
by
njornet
▴ 20
No... the extracted sample is already a mix so no way to barcode
Comment: Very low RNA splicing rate for pulmonary AT2 cells
by
e.r.zakiev
▴ 200
For anyone it might be useful: a colleague of mine, who was not dumb to use the wrong annotation `gtf`, also observed an important issue of…
Answer: Very low RNA splicing rate for pulmonary AT2 cells
by
e.r.zakiev
▴ 200
Hello people sorry I am dumb the problem lied in the fact that I had mouse cells but my `.gtf` transcriptome file was for the human. Now wi…
Comment: Genbank File Format
by
GenoMax
141k
Can you indicate if you need to do this within CLC or can use an external solution (if someone provides it here). If you need to do this in…
Comment: Downsampling fastq file
by
Ram
43k
The file being PE should not matter. I'd recommend you open an issue on the seqtk github repo as this is starting to look like some sort of…
Comment: CWl and toil singularity image e.g busybox? Thank you
by
Ram
43k
Do the developers of toil mention biostars? Where do they direct their support requests to?
Comment: How should I make kallisto indexes?
by
dsull
★ 5.9k
As an additional note, all those ``--include-attribute`` stuff was basically to restrict the transcriptome to precisely the items that Cell…
Answer: How should I make kallisto indexes?
by
dsull
★ 5.9k
I recommend the ``kb ref`` method for two reasons: 1. The index created will yield more accurate mapping for datasets that have a substa…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
Were these samples barcoded when they were run. If not then you won't be able to do much.
Comment: ScRNA data question
by
bk11
★ 2.4k
The approach you are using here is the old method. Seurat is updated to V5. Please try Seurat V5 integrative analysis described in the link…
Answer: How should I make kallisto indexes?
by
Bajaj
• 0
Hi, you can still use `kallisto index -i transcripts.index transcripts.fa` (extract the gz file) for making index files. I have tried it an…
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