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116,906 results • Page
1 of 2339
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36
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How to process Bulk WES data?
WES
WGS
updated 48 minutes ago by
GenoMax
142k • written 1 hour ago by
wyuan37
• 0
0
votes
0
replies
25
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
2 hours ago by
cedric.blais
• 0
0
votes
2
replies
339
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
2 hours ago by
David Langenberger
11k
0
votes
1
reply
43
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 59 minutes ago by
Ram
43k • written 3 hours ago by
eking28
• 0
1
vote
4
replies
312
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 2 hours ago by
GenoMax
142k • written 5 days ago by
Prawesh
• 0
1
vote
3
replies
289
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
3 hours ago by
kalavattam
▴ 190
795
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
117
views
How to interpret infinite odds ratio?
statistics
updated 4 hours ago by
bhumm
▴ 140 • written 9 hours ago by
Lukas
• 0
0
votes
2
replies
80
views
Duplicated sequence samtools
bowtie2
samtools
updated 4 hours ago by
GenoMax
142k • written 5 hours ago by
Moinuddin
• 0
0
votes
0
replies
37
views
reference-free assembly error assessment tools
assembly
5 hours ago by
lagartija
▴ 160
1
vote
2
replies
120
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
updated 5 hours ago by
lagartija
▴ 160 • written 11 hours ago by
Esraa
• 0
1
vote
0
replies
41
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
6 hours ago by
J.
▴ 10
0
votes
0
replies
53
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
6 hours ago by
Biostar
2.7k
0
votes
1
reply
64
views
Splitting Seurat object by sample layers
seurat
updated 1 hour ago by
Ram
43k • written 7 hours ago by
kilcdincer
▴ 10
0
votes
2
replies
85
views
Galaxy StringTie error
stringtie
galaxy
updated 1 hour ago by
Ram
43k • written 7 hours ago by
trkfs
• 0
0
votes
0
replies
46
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
9 hours ago by
atariw
▴ 10
0
votes
1
reply
96
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 9 hours ago by
GenoMax
142k • written 19 hours ago by
octpus616
▴ 100
0
votes
1
reply
79
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 9 hours ago by
Juke34
8.6k • written 10 hours ago by
Vijith
▴ 30
0
votes
1
reply
92
views
consensus sequence calling
consensus
updated 6 hours ago by
bk11
★ 2.4k • written 10 hours ago by
Ghada
• 0
0
votes
3
replies
118
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 1 hour ago by
Ram
43k • written 11 hours ago by
yau
• 0
3
votes
2
replies
207
views
imputation through beagle
panel
beagle
reference
imputation
5 hours ago by
analyst
▴ 50
0
votes
0
replies
47
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
11 hours ago by
JACKY
▴ 140
0
votes
1
reply
346
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 11 hours ago by
aw7
▴ 280 • written 24 days ago by
abhishekghadge
• 0
1
vote
1
reply
163
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 11 hours ago by
aw7
▴ 280 • written 4 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
59
views
Reference panel of normals for ensembl named refgenome
Mutect2
12 hours ago by
gernophil
▴ 80
1
vote
0
replies
54
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
13 hours ago by
tomas4482
▴ 400
2
votes
3
replies
200
views
BWA alignment
Samtools
bam
13 hours ago by
Vahid
• 0
3
votes
2
replies
128
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 13 hours ago by
ATpoint
82k • written 14 hours ago by
jennyp0706
• 0
0
votes
1
reply
122
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 14 hours ago by
Philipp Bayer
8.4k • written 1 day ago by
samRayne
• 0
0
votes
1
reply
207
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 50 minutes ago by
Ram
43k • written 4 days ago by
Nikki
• 0
2
votes
13
replies
2.8k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 16 hours ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
159
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 17 hours ago by
chrchang523
10k • written 5 days ago by
analyst
▴ 50
0
votes
0
replies
74
views
lncRNA
tcga
lncrna
17 hours ago by
jain72744
▴ 10
0
votes
1
reply
205
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
jain72744
▴ 10
2
votes
5
replies
509
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 1 day ago by
arctic
▴ 40 • written 10 days ago by
M.
▴ 30
1
vote
2
replies
294
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq
limma
RNA-seq
removeBatchEffect
batch-effect
updated 7 hours ago by
Ram
43k • written 1 day ago by
t.fortunato.asquini
• 0
2
votes
1
reply
225
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 1 day ago by
pjb39
▴ 210 • written 3 days ago by
beantkapoor16
▴ 10
0
votes
2
replies
176
views
Output file of samtools flagstat empty
samtools-flagstat
updated 13 hours ago by
colindaven
6.4k • written 1 day ago by
ramendra.sarma
• 0
0
votes
0
replies
91
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot
PCAtools
deseq2
pca
1 day ago by
BioinfGuru
★ 1.7k
2
votes
8
replies
301
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
105
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
1 day ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
212
views
input file in rmats
rmats
updated 1 day ago by
Mathew
▴ 120 • written 3 days ago by
Lambodarswain316
• 0
2
votes
2
replies
257
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
9 hours ago by
Christopher
• 0
6
votes
7
replies
328
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
1 day ago by
sansan_96
▴ 90
2
votes
3
replies
235
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
12 hours ago by
Azra
▴ 10
2
votes
1
reply
208
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
melissachua90
▴ 70
9
votes
7
replies
7.1k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 2 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
0
votes
4
replies
350
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
15 hours ago by
beginner123
• 0
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic
paired-end
updated 2 days ago by
Ruqaiya
• 0 • written 6.4 years ago by
dllopezr
▴ 130
0
votes
2
replies
207
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
15 hours ago by
analyst
▴ 50
116,906 results • Page
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Recent Votes
Best way to query VCF for specific variants
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
A: Is Bam One-Based Or Zero-Based?
A: Is Bam One-Based Or Zero-Based?
A: Data Set Suitable For Comparing Wgs, Exome, And Rna-Seq Data Generated From The
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
Practical Haplotype Graph v2 not finding correct paths
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Comment: SNPEff database building error
by
Fungal genetics
• 0
Hi, Below SNPEff database building error I am getting. "FATAL ERROR: Most Exons do not have sequences!" The headers are correct and sam…
Comment: Extracting named fasta sequences according to list with Biopython
by
Rubayetul
• 0
the last line of SeqIO.write(record.....'fasta') in a for loop will input the the last record into new fasta file and it will only contain …
Comment: How to process Bulk WES data?
by
GenoMax
142k
You could use `sarek` (nf-core's exome pipeline) if you don't want to customize or reinvent : https://nf-co.re/sarek/3.4.2
Comment: Empty .best and .sing2 Files After Running Demuxlet
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac
by
David Langenberger
11k
Two last seats have just become available. Apply now, if you want them.
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
GenoMax
142k
You always need to add the following option when you are using `-p` to count paired-end reads. --countReadPairs If specified, fragm…
Comment: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t
by
mropri
▴ 150
Hi swbarnes2, that was the problem, they were not numeric but as character columns. converted them and it fixed the error. Thank you for yo…
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Prawesh
• 0
I figured out: Since featureCounts counts fragments and not reads, we have pair-end data that means **Assigned** value from the output w…
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
kalavattam
▴ 190
> My question is this: "mate reverse strand" (flag 16/0x10) or "read reverse strand" (flag 32/0x20) do not directly relate to the strandedn…
Answer: How to interpret infinite odds ratio?
by
bhumm
▴ 140
As you stated, your problem is likely division by 0. See this [Cross-Validated][1] post that seems to be very similar to your problem. In …
Comment: Duplicated sequence samtools
by
GenoMax
142k
Consider using SLURM job arrays if you want to use a `for` loop inside a single SLURM job: https://hpc.nmsu.edu/discovery/slurm/job-arrays/
Answer: Duplicated sequence samtools
by
Pierre Lindenbaum
161k
the sequence c_000007023807_aloha2_low_cov is duplicated in the reference grep c_000007023807_aloha2_low_cov path/to/reference.fasta
Comment: imputation through beagle
by
analyst
▴ 50
Thank you so much dthorbur. Yes I am new to imputation analysis. I will follow your kind suggestions. Thanks again!
Answer: Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
by
lagartija
▴ 160
I don't know but another way of doing it would be to combine different datasets of different strains that you know are clonal. Then you kno…
Comment: consensus sequence calling
by
bk11
★ 2.4k
Please check out these posts https://www.biostars.org/p/367626/
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