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552 results • Page
2 of 12
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Views
Votes
Replies
0
votes
8
replies
338
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 3 days ago by
GenoMax
129k • written 4 days ago by
Marta
• 0
1
vote
2
replies
198
views
Combination of ROC CURVE
roccurve
R
AUC
21 hours ago by
Maria17
▴ 20
1
vote
0
replies
90
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
4 days ago by
Jonathan Lefebre
▴ 50
0
votes
3
replies
178
views
DEGseq for multiple samples
DEGseq
DEG
updated 4 days ago by
Ram
39k • written 4 days ago by
ALOUSH ALI
• 0
0
votes
0
replies
78
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 4 days ago by
Ram
39k • written 4 days ago by
Rishabh Jha
• 0
1
vote
3
replies
204
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 4 days ago by
GenoMax
129k • written 4 days ago by
NikhilP
▴ 20
2
votes
2
replies
181
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
CD
analysis
bioinformatic
Protocol
updated 4 days ago by
Dr William Klubinski
▴ 80 • written 4 days ago by
linnet.roque6
▴ 10
3
votes
12
replies
2.1k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 3 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
0
votes
0
replies
103
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
4 days ago by
mbk0asis
▴ 660
0
votes
0
replies
96
views
PRSice-2 using SNPs with extremely low P-value
PRSice-2
SNP
4 days ago by
Apprentice
▴ 140
0
votes
0
replies
302
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
4 days ago by
Vincent Laufer
★ 2.9k
0
votes
0
replies
104
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 4 days ago by
Ram
39k • written 4 days ago by
Mah
• 0
1
vote
3
replies
217
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 4 days ago by
GenoMax
129k • written 4 days ago by
mls
• 0
0
votes
0
replies
106
views
snpEff error. No CDS checked
snpEff
gtf
WES
5 days ago by
fifty_fifty
▴ 40
0
votes
0
replies
106
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
5 days ago by
Maddie
• 0
1
vote
2
replies
206
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
3 days ago by
rheab1230
▴ 140
2
votes
4
replies
234
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 4 days ago by
Ram
39k • written 5 days ago by
miguellarrazlopezdenovales
• 0
1
vote
0
replies
106
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
5 days ago by
fr
▴ 200
0
votes
2
replies
173
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 5 days ago by
rpolicastro
12k • written 5 days ago by
Pac314
▴ 10
0
votes
2
replies
163
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
4 days ago by
survive
• 0
1
vote
1
reply
127
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 5 days ago by
GenoMax
129k • written 5 days ago by
hashim.rana11
▴ 20
0
votes
0
replies
80
views
metagenomics data - AMR genes
amr
resistome
resistance
ARG
metagenomics
5 days ago by
aziznasr1920
▴ 10
1
vote
3
replies
184
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 4 days ago by
Pierre Lindenbaum
154k • written 5 days ago by
herh
• 0
0
votes
0
replies
74
views
1000G reference panel for LD clumping
LD
5 days ago by
en_keser
• 0
0
votes
0
replies
84
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
5 days ago by
saladi
▴ 30
0
votes
2
replies
609
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 6 days ago by
Ram
39k • written 13 months ago by
Meeran
• 0
0
votes
7
replies
566
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 5 days ago by
Vincent Laufer
★ 2.9k • written 9 days ago by
Camilo Andres
▴ 30
0
votes
3
replies
202
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 5 days ago by
andres.firrincieli
3.4k • written 6 days ago by
kamanovae
▴ 80
0
votes
1
reply
154
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 6 days ago by
GenoMax
129k • written 6 days ago by
fafad046
• 0
0
votes
3
replies
190
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
4 days ago by
Mohd
▴ 20
1
vote
2
replies
177
views
sorting BAM file
BAM
updated 5 days ago by
ATpoint
72k • written 6 days ago by
Mohammad Amin
• 0
0
votes
0
replies
88
views
Converting rds file to h5ad and saving raw counts as X
R
seurat
updated 6 days ago by
zx8754
11k • written 6 days ago by
sidrah.maryam
▴ 50
0
votes
1
reply
147
views
Seurat: How to get all genes name of a cell ?
seurat
updated 5 days ago by
jv
★ 1.2k • written 6 days ago by
Picasa
▴ 640
1
vote
0
replies
234
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 5 days ago by
Ram
39k • written 6 days ago by
Supernova
• 0
0
votes
0
replies
102
views
Bulk RNA sequencing time course pathway analysis progression visualization
time-course
RNA-seq
pathway
updated 6 days ago by
Ram
39k • written 6 days ago by
Fred
• 0
2
votes
2
replies
113
views
how to use Hemtools bed2vcf?
vcf
linux
conversion
bed
updated 6 days ago by
Pierre Lindenbaum
154k • written 6 days ago by
MobiusT
▴ 10
0
votes
1
reply
149
views
How to calculate SARS-2'S evolutionary rate
evolutionary-rate
updated 6 days ago by
Ram
39k • written 6 days ago by
chengc2016zzu
• 0
0
votes
0
replies
84
views
How to retrieve non-redundant restriction enzymes database from Rebase?
Rebase
Databases
enzymes
Restriction
6 days ago by
Mahmoud Reda
▴ 10
1
vote
2
replies
202
views
Converting RefSeq protein accession IDs into entreZ IDs
RNA-SEQ
5 days ago by
Pegasus
▴ 90
0
votes
0
replies
120
views
Merging multiple PLINK files
plink
merging
7 days ago by
Nejla
• 0
0
votes
0
replies
118
views
References selected by ExomeDepth CNV
CNV
ExomeDepth
updated 7 days ago by
GenoMax
129k • written 7 days ago by
keiko.asakura
• 0
0
votes
2
replies
224
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
5 days ago by
J.F.Jiang
▴ 900
0
votes
2
replies
203
views
Upstream pseudogene causing MAPQ 0 and exclusion during variant calling
Mapping
Variant-calling
masking
updated 7 days ago by
Ram
39k • written 7 days ago by
Joel Wallenius
▴ 130
1
vote
3
replies
702
views
Regular Expression for conversion
Linux
grep
updated 6 days ago by
Joe
21k • written 19 months ago by
shabbas12
▴ 10
0
votes
1
reply
167
views
weird behaviour on bedtools
bedtools
RNA-Seq
updated 5 days ago by
Ram
39k • written 7 days ago by
barrypraveen
▴ 110
0
votes
2
replies
174
views
fgsea/clusterProfiler Packages for nCounter data enrichment analysis
nanostring
gsea
r
7 days ago by
pg45863
• 0
0
votes
1
reply
139
views
ABySS Process Killed
ABySS
genome
assembly
updated 7 days ago by
GenoMax
129k • written 7 days ago by
asarcillo
• 0
0
votes
0
replies
99
views
Cell type sub-clustering across multiple samples in scRNA-seq
scRNA-seq
7 days ago by
narges.bioinf
• 0
0
votes
3
replies
225
views
Query qbout single cell sequencing
fastq
ScRNA
updated 6 days ago by
Ram
39k • written 7 days ago by
abbas.waseem.gcu
▴ 20
0
votes
1
reply
187
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 6 days ago by
fracarb8
▴ 950 • written 7 days ago by
Sun
• 0
552 results • Page
2 of 12
Recent Votes
Answer: Perl script running slow with big files
C: Bedtools problem : It looks as though you have less than 3 columns at line: 1.
A: Forward And Reverse Strand Conventions
Comment: hisat2 Error 137
Comment: NCBI API, Perl
Comment: Is hg38 on the multiz 30-way alignment inaccurate?
Answer: Is it possible to add a dendrogram as a top annotation using ComplexHeatmap ?
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Comment: calculate p value and associated z score for snp-gene pair
by
LChart
2.6k
I think researchers would agree that FDR > 0.05 is not significant, though some would argue FDR between 0.05 and 0.1 is OK for an initial f…
Comment: Trying to edit VCF file
by
Pierre Lindenbaum
154k
> When I opened the vcf in excel I noticed that there was still columns for what I removed from the file. please, explain, show the data.…
Comment: hisat2 Error 137
by
Forough
▴ 10
Thank you very much for sending the like. I will try it.
Comment: Which method is the best for using in "dba.count" in Diffbind R package
by
Jo
• 0
Thank you for all the helpful advice and explanations. Can you further explain this part: > "The default normalization factors (based sol…
Comment: VEP tab/vcf - Different output
by
Ram
39k
I don't think so, no. EnsEMBL seems to have come up with a verbose explanation for why they don't want to put in the effort.
Comment: VEP tab/vcf - Different output
by
Jeremy Leipzig
21k
is there any way to report the VCF-style ref and alt in the VEP tabular output?
Comment: Is hg38 on the multiz 30-way alignment inaccurate?
by
Daniel
▴ 30
Thank you! If I understand correctly, it's possible that the coordinates/sequences may not be the same anymore, because the maf files use t…
Comment: NCBI API, Perl
by
alessandro.alma00
• 0
Sorry i didn't want to be rude.. Thank you for helping me, im sorry but its the first time I use API tbh... i will like to retrieve the seq…
Comment: How to perform statistical analysis of label free experiment using results from
by
Ram
39k
Do not add answers unless you're actually answering the question. Use `Add Comment` instead. I've moved your post this time, be careful in …
Answer: Is it possible to add a dendrogram as a top annotation using ComplexHeatmap ?
by
jv
★ 1.2k
this [chapter](https://jokergoo.github.io/ComplexHeatmap-reference/book/index.html) of the ComplexHeatmap reference makes it look like you …
Comment: Is hg38 on the multiz 30-way alignment inaccurate?
by
GenoMax
129k
Not sure if this is relevant: https://www.biostars.org/p/9555543/
Comment: How to quantification proteomics data
by
eqoa45
• 0
Hello, can I ask how did you manage the solution?
Comment: How to perform statistical analysis of label free experiment using results from
by
eqoa45
• 0
Hello, i'm dealing with the same question. How did you manage your data at the end? I was thinking that I don't need to do any extra proces…
Comment: CHiP-Seq Questions
by
jared.andrews07
★ 14k
Sounds like you should do some QC of your ChIP-seq data first to ensure the assay actually worked.
Answer: Perl. How to retrieve data until a keyword in GenBank?
by
JC
13k
The trick over here is to start capturing when you found "LOCUS" and stop when you found "COMMENT", something like: #!/usr/bin/perl …
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