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116,992 results • Page
3 of 2340
Sort: Rank
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Votes
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0
votes
1
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149
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 3 days ago by
Ram
43k • written 3 days ago by
eking28
• 0
2
votes
5
replies
491
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 2 days ago by
Ram
43k • written 8 days ago by
Prawesh
• 0
1
vote
3
replies
432
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 days ago by
kalavattam
▴ 190
1
vote
2
replies
266
views
How to interpret infinite odds ratio?
statistics
3 days ago by
Lukas
• 0
1
vote
2
replies
179
views
Duplicated sequence samtools
bowtie2
samtools
updated 3 days ago by
GenoMax
142k • written 3 days ago by
Moinuddin
• 0
0
votes
0
replies
104
views
reference-free assembly error assessment tools
assembly
3 days ago by
lagartija
▴ 160
2
votes
4
replies
293
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq
vcf
variant-calling
2 days ago by
Esraa
• 0
2
votes
0
replies
141
views
Herald:
The Biostar Herald for Monday, May 13, 2024
herald
3 days ago by
Biostar
2.8k
0
votes
1
reply
142
views
Splitting Seurat object by sample layers
seurat
updated 3 days ago by
Ram
43k • written 3 days ago by
kilcdincer
▴ 10
0
votes
4
replies
257
views
Galaxy StringTie error
stringtie
galaxy
3 days ago by
trkfs
• 0
0
votes
0
replies
103
views
dbNSFP sift scores integration
SIFT
VEP
dbNSFP
3 days ago by
atariw
▴ 10
0
votes
1
reply
153
views
Mouse ribosome sequences in fasta format
fasta
mm10
rRNA
updated 3 days ago by
GenoMax
142k • written 4 days ago by
octpus616
▴ 100
1
vote
4
replies
343
views
Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus
annotation
assembly
genome
updated 2 days ago by
Juke34
8.6k • written 3 days ago by
Vijith
▴ 30
0
votes
1
reply
161
views
consensus sequence calling
consensus
updated 3 days ago by
bk11
★ 2.5k • written 4 days ago by
Ghada
• 0
0
votes
3
replies
190
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat
single-cell
scRNA-seq
R
updated 3 days ago by
Ram
43k • written 4 days ago by
yau
• 0
3
votes
2
replies
278
views
imputation through beagle
panel
beagle
reference
imputation
3 days ago by
analyst
▴ 50
0
votes
0
replies
88
views
Empty kernel in SEACells model
single-cell
scanpy
seacells
python
anndata
4 days ago by
JACKY
▴ 140
0
votes
1
reply
533
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools
gcs
updated 4 days ago by
aw7
▴ 300 • written 27 days ago by
abhishekghadge
• 0
3
votes
1
reply
216
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair
samtools
alignment
updated 4 days ago by
aw7
▴ 300 • written 8 days ago by
Zeng Hao
▴ 40
0
votes
0
replies
101
views
Reference panel of normals for ensembl named refgenome
Mutect2
4 days ago by
gernophil
▴ 80
1
vote
0
replies
96
views
Producing sequence for splicing isoforms
isoform
rMATs
splicing
alternative
SplAdder
4 days ago by
tomas4482
▴ 400
2
votes
6
replies
380
views
BWA alignment
Samtools
bam
updated 2 days ago by
a.alnawfal.1992
▴ 260 • written 4 days ago by
Vahid
• 0
3
votes
2
replies
189
views
Publish a Letter in higher impact vs Research article in lower impact
Article
Letter
Journal
updated 4 days ago by
ATpoint
82k • written 4 days ago by
jennyp0706
• 0
0
votes
1
reply
157
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence
university
assembly
protein
genomics
updated 4 days ago by
Philipp Bayer
8.5k • written 4 days ago by
samRayne
• 0
0
votes
1
reply
245
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Mendelian-Randomization
updated 3 days ago by
Ram
43k • written 7 days ago by
Nikki
• 0
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
0
votes
1
reply
194
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
updated 4 days ago by
chrchang523
10k • written 9 days ago by
analyst
▴ 50
0
votes
0
replies
109
views
lncRNA
tcga
lncrna
4 days ago by
jain72744
▴ 10
0
votes
1
reply
242
views
Nomalization - TCGA, RNA-seq and Microarray
TCGA
RNA-seq
Nomalization
Microarray
updated 4 days ago by
Zhenyu Zhang
★ 1.2k • written 7 days ago by
jain72744
▴ 10
2
votes
5
replies
567
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 4 days ago by
arctic
▴ 40 • written 13 days ago by
M.
▴ 30
1
vote
2
replies
358
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 3 days ago by
Ram
43k • written 4 days ago by
t.fortunato.asquini
• 0
2
votes
1
reply
261
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
updated 4 days ago by
pjb39
▴ 210 • written 6 days ago by
beantkapoor16
▴ 10
0
votes
2
replies
209
views
Output file of samtools flagstat empty
samtools-flagstat
updated 4 days ago by
colindaven
6.4k • written 4 days ago by
ramendra.sarma
• 0
2
votes
8
replies
377
views
joint callset and vcf sorting, unknown TAG issue
sort
bcftools
GLNexus
merge
VCF
updated 4 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
Matteo Ungaro
▴ 100
0
votes
0
replies
128
views
News:
Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore
RNAseq
5 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
230
views
input file in rmats
rmats
updated 5 days ago by
Mathew
▴ 140 • written 7 days ago by
Lambodarswain316
• 0
3
votes
3
replies
359
views
Kraken2 database
kraken
microbialdb
database
krakendb
kraken2
updated 3 days ago by
Mathew
▴ 140 • written 6 days ago by
Christopher
• 0
6
votes
7
replies
385
views
Longest transcript variant per gene
transcript
longest
variant
orthofinder
4 days ago by
sansan_96
▴ 90
2
votes
3
replies
277
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio
Cibersort
R
4 days ago by
Azra
▴ 10
2
votes
1
reply
232
views
Failed to open VCF file
GATK
sentieon
BWA-MEM
updated 6 days ago by
Pierre Lindenbaum
161k • written 6 days ago by
melissachua90
▴ 70
9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 6 days ago by
Ruqaiya
• 0 • written 5.7 years ago by
xiaozhongzhiping
▴ 20
0
votes
4
replies
397
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
4 days 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 6 days ago by
Ruqaiya
• 0 • written 6.5 years ago by
dllopezr
▴ 130
0
votes
2
replies
229
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated
java.nio.bufferunderflowexception
haplotypecaller
bqsr
4 days ago by
analyst
▴ 50
0
votes
6
replies
419
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp
vcf
genomics
plink
updated 3 days ago by
Ram
43k • written 6 days ago by
ajbarrett98
• 0
0
votes
11
replies
533
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
4 days ago by
Tuck898
• 0
3
votes
3
replies
280
views
what is another word for a BLAST "hit"?
blast
alignment
6 days ago by
dec986
▴ 380
0
votes
1
reply
204
views
extract viral protein of interest from 10k whole viral genomes
nBLAST
viral-genome
updated 6 days ago by
Ram
43k • written 6 days ago by
Shwetha
• 0
0
votes
0
replies
164
views
Marker Features variance by cluster, sample, and treatment group
Seurat
scATAC-seq
ArchR
updated 6 days ago by
Ram
43k • written 6 days ago by
naomiboldon
• 0
1
vote
3
replies
283
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk
vcf
liftover
updated 6 days ago by
Ram
43k • written 6 days ago by
Omics data mining
▴ 260
116,992 results • Page
3 of 2340
Recent Votes
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
Answer: Details on salmon index
Answer: Generating consensus sequence from bam file
Answer: Short Read Data Genome Assembly
Comment: API kegg - IndexError: list index out of range
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Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
You can have a look on my answer. I have post it below.
Answer: In one PCA plot, can I calculate the percentage of different factors that contri
by
diqixiaoyaoer
▴ 20
Here is my script that can be used to calculate how much degree that different factors contribute to PCA variance (PC1 and PC2). # …
Comment: Details on salmon index
by
Lorenzo
• 0
Thank you so much for the beautiful explanation. Just one more curiosity. So in the first versions Salmon utilized RapMap to index and then…
Comment: What marks a De-Novo Genome assembly as FAILED?
by
dthorbur
★ 2.0k
I'm a little confused about your experimental design. Are you making 45 different assemblies? Or are all the samples from the same individu…
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ATpoint
82k
You should be stating how you constructed the index, and include the actual lines for the problematic genes from the abundance files. Note …
Comment: zero TPM for many gene including housekeeping when using kallisto
by
dariober
14k
You could try [salmon](https://combine-lab.github.io/salmon/getting_started/) to see if the problem is with kallisto or with the pseudo-ali…
Comment: solution-Transcriptome.cpp:18:Transcriptome: exiting because of *INPUT FILE* err
by
GenoMax
142k
> INPUT FILE error: could not open input file /geneInfo.tab Based on the error it appears that the input file you are providing could not …
Answer: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP
by
kilcdincer
▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
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