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113,962 results • Page
1 of 2280
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0
votes
0
replies
15
views
ASEReadCounter output wrong number of coverage
ASEReadCounter
2 hours ago by
junhuili
• 0
1
vote
5
replies
749
views
Strandedness of RNA-seq results
dual-RNA-seq
featurecounts
strandedness
HISAT2
updated 1 hour ago by
charles.feigin
• 0 • written 18 months ago by
jamesymtang
▴ 10
1
vote
1
reply
935
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 1 hour ago by
charles.feigin
• 0 • written 6 weeks ago by
xinrantian
▴ 20
0
votes
0
replies
37
views
megablast taxonomy assign in blobtools
blobtools
4 hours ago by
bs
• 0
0
votes
0
replies
51
views
Aligning sequences with multiple genetic codes!
genetic_codes
codon
MEGA11
alignment
7 hours ago by
George X.
• 0
0
votes
0
replies
54
views
How to use Nextflow to call scripts from different environments?
wrapper
environments
anaconda
conda
nextflow
8 hours ago by
O.rka
▴ 710
773
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
0
votes
1
reply
79
views
Cell ranger multi for demultiplexing FB files and GEX files
ranger
multi
cell
updated 4 hours ago by
GenoMax
136k • written 8 hours ago by
Shloka
• 0
2
votes
2
replies
141
views
Calculate GC content for entire chromosome
bam
GC
assembly
bwa-mem
updated 10 hours ago by
ATpoint
78k • written 13 hours ago by
skilleta0527
• 0
0
votes
0
replies
53
views
Ambient RNA removal method that generates whole (integer) counts
pseudobulk
soupX
DESeq2
single-cell
10 hours ago by
EK
• 0
0
votes
1
reply
89
views
Software for Spatial Transcriptomic data [NanoString; Visium]?
NanoString
Visium
Spatial-Transcriptomics
10X
5 hours ago by
LauferVA
3.8k
4
votes
15
replies
6.3k
views
8 follow
bbmap split paired-end reads back into separated fastq files?
genome
next-gen-sequencing
bbmap
alignment
updated 4 hours ago by
GenoMax
136k • written 5.2 years ago by
c.e.chong
▴ 60
0
votes
1
reply
118
views
AssemblyMAFFromAnchorWavePlugin IndexOutOfBoundsException
phg
updated 12 hours ago by
lcj34
▴ 250 • written 17 hours ago by
ryan
• 0
1
vote
1
reply
93
views
ANNOVAR Download Failing
ANNOVAR
updated 10 hours ago by
Ram
41k • written 12 hours ago by
tony
• 0
0
votes
1
reply
106
views
Sorted bam files are empty after sorting them from bam
bam
dna
updated 10 hours ago by
Ram
41k • written 13 hours ago by
mgranada3
▴ 30
0
votes
2
replies
146
views
Downsampling ATAC-seq BAM files
ATAC-seq
9 hours ago by
Elise
• 0
0
votes
0
replies
56
views
spatial metabolomics, python
spatial-metabolomics
updated 13 hours ago by
Ram
41k • written 13 hours ago by
joha
▴ 10
0
votes
3
replies
291
views
RNA seq
Differential-gene-expression
updated 14 hours ago by
jv
★ 1.3k • written 2 days ago by
Byonkesh
• 0
0
votes
4
replies
403
views
Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom
RNAseq
differential-gene-expession
limma
batch-effect
updated 14 hours ago by
Ram
41k • written 4 days ago by
fluke
• 0
1
vote
4
replies
166
views
Feasibility of Enrichment Analysis from RTqPCR results
GO
RT-qPCR
Enrichment-Analysis
updated 1 hour ago by
GenoMax
136k • written 16 hours ago by
Javier
• 0
0
votes
0
replies
70
views
WGCNA for different tissues
WGCNA
Worms
RNA-Seq
16 hours ago by
kdca
• 0
0
votes
2
replies
121
views
Issues while running blastx
blastx
RNA-seq
updated 1 hour ago by
GenoMax
136k • written 19 hours ago by
Foad
▴ 10
0
votes
1
reply
99
views
Tophat2 Error running 'long_spanning_reads' on M1 Mac
Tophat2
Boost
RiboSeq
M1-Mac
updated 14 hours ago by
Ram
41k • written 18 hours ago by
riboseq938
• 0
0
votes
1
reply
130
views
Contrasts in R
contrasts
r
updated 14 hours ago by
jv
★ 1.3k • written 17 hours ago by
SGMS
▴ 130
1
vote
5
replies
611
views
ATAC-Seq and RPKM
RPKM
ATAC-Seq
updated 17 hours ago by
ATpoint
78k • written 9 weeks ago by
qudrat.nii
• 0
0
votes
1
reply
1.3k
views
Correlation RNA-seq and ATAC-seq
RNA-Seq
R
gene
updated 18 hours ago by
Tao Zhu
▴ 10 • written 3.4 years ago by
pastel950818
• 0
5
votes
4
replies
843
views
Methods to integrate ATAC-seq and RNA-seq
RNA-seq
ATAC-seq
updated 18 hours ago by
Tao Zhu
▴ 10 • written 4 months ago by
Chris
▴ 230
0
votes
1
reply
108
views
Issues with Chromosome Encoding and VCF Annotation in dbSNP Alpha Release
bcftools
dbSNP
tabix
vcf
updated 14 hours ago by
Ram
41k • written 18 hours ago by
Fernando
• 0
0
votes
1
reply
266
views
How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes
MLST
phylogenetic
nanopre
updated 18 hours ago by
Joe
21k • written 19 hours ago by
Ralph
• 0
1
vote
2
replies
151
views
contrast file in DESeq2 bioconductor
DEseq2
updated 14 hours ago by
Ram
41k • written 19 hours ago by
r.shiasi3897
▴ 10
1
vote
3
replies
254
views
Best method for batch correction of three datasets
RNA-seq
2 hours ago by
CTLong
▴ 20
0
votes
1
reply
116
views
How to remove 3rd codon positions in a multiple sequence allignment?
i
updated 14 hours ago by
Ram
41k • written 19 hours ago by
francesco.degiglio
• 0
0
votes
0
replies
76
views
Classification ML model using different type of data
machine-learning
transcriptomics
R
python
biomarkers
19 hours ago by
sil_bioinfo
▴ 40
0
votes
0
replies
66
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
21 hours ago by
Saad Khan
▴ 420
0
votes
0
replies
65
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
21 hours ago by
Adrian
• 0
1
vote
7
replies
262
views
How to download multiple genome files using command line (MacOS) using datasets
ncbi-datasets
Bacteria
Genome
updated 11 hours ago by
Ram
41k • written 23 hours ago by
scholaraspect2008
• 0
3
votes
1
reply
124
views
GEO dataset Microarray data analysis help
R
microarray
NCBI
GEO
updated 14 hours ago by
Ram
41k • written 23 hours ago by
Confused_human
▴ 20
0
votes
3
replies
169
views
Microarray batch correction method suggestions
microarray
batch-correction
updated 10 hours ago by
Ram
41k • written 1 day ago by
Sumeet
• 0
0
votes
0
replies
77
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
1 day ago by
Clayton
• 0
0
votes
0
replies
80
views
Enzyme commission number in ncbi Gene database
enzyme-commission-number
updated 14 hours ago by
Ram
41k • written 1 day ago by
Maatary
• 0
2
votes
1
reply
153
views
Best way to normalize transcript reads data for PCA & correlation and further biostat analysis
transcript_reads
updated 1 day ago by
Jeremy
▴ 860 • written 1 day ago by
Faith
▴ 40
2
votes
2
replies
151
views
Help with gatk CreateSequenceDictionary
GATK
updated 1 day ago by
GenoMax
136k • written 1 day ago by
Chris
▴ 230
2
votes
5
replies
328
views
FastQC without yellow box
fastqc
updated 14 hours ago by
Ram
41k • written 1 day ago by
lobelino
• 0
0
votes
1
reply
133
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 1 day ago by
Brian Bushnell
20k • written 1 day ago by
isMM
• 0
2
votes
4
replies
231
views
error when installing gistic2 using conda
conda
gistic2
updated 10 hours ago by
Ram
41k • written 1 day ago by
luckyday1661
• 0
0
votes
0
replies
98
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 1 day ago by
Ram
41k • written 1 day ago by
boone5jones
• 0
0
votes
0
replies
84
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
1 day ago by
S
• 0
3
votes
2
replies
235
views
RNA-seq log2 fold change to linear
RNA-seq
DGE
updated 1 day ago by
jared.andrews07
★ 16k • written 1 day ago by
hmiller
• 0
74
votes
32
replies
4.8k
views
12 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 1 day ago by
Ram
41k • written 6 months ago by
Sasha
▴ 770
0
votes
2
replies
195
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 23 hours ago by
ATpoint
78k • written 1 day ago by
wangjb702
• 0
113,962 results • Page
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Recent Votes
Strandedness of RNA-seq results
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
Answer: How to create a mutation frequency comparison plot?
Comment: Best method for batch correction of three datasets
Answer: Calculate GC content for entire chromosome
How Much Coverage Do We Need For An Rna-Seq Experiment?
Answer: Calculate GC content for entire chromosome
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Recent Replies
Comment: Issues while running blastx
by
GenoMax
136k
> ~/Downloads/uniprot_sprot.dat `dat` files are not blast index ready. You should download the `fasta` format file and create your own bla…
Comment: Strandedness of RNA-seq results
by
charles.feigin
• 0
Hi, coming here for the same reason. Libraries prepared with the Illumina Stranded mRNA Prep kit (dUTP-based). In hisat2 with --rf I get <…
Comment: How to interpret the discrepancy of assignment rate in featurecounts using forwa
by
charles.feigin
• 0
I'm having this exact same problem. PolyA RNA-Seq library, running with --fr in hisat2 gives a high fraction of concordant single-mappers, …
Comment: How to create a mutation frequency comparison plot?
by
saipra003
▴ 10
That's awesome thank you. Found out after a bit of researching that this is called a `Cleveland Dot Plot` if anyone else comes across this.
Comment: Cell ranger multi for demultiplexing FB files and GEX files
by
GenoMax
136k
Demultiplexing is typically done using Illumina software? Have you done this already?: https://www.10xgenomics.com/support/software/cell-ra…
Comment: bbmap split paired-end reads back into separated fastq files?
by
GenoMax
136k
If you simply want to merge "technical" sequencing replicates then you can do the following cat file1_R1.fastq file1_R1.fastq > merged…
Comment: Best method for batch correction of three datasets
by
CTLong
▴ 20
Thanks for the very descriptive reply. I will give it a try nonetheless because this is pretty much the only way to account for the biologi…
Comment: Installing and importing viennaRNA to python in windows
by
Yun
• 0
Just delete "subprocess.", use p = Popen('RNAfold.exe', stdin=PIPE, stdout=PIPE) instead.
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
by
peanut
• 0
"Okay.Thank you very much."
Comment: Genome coverage of MAGs while submitting to NCBI
by
wn835166087
• 0
Hi, I have a follow up question about this. During my binning process, I obtained the coverage of each contig. Can I take the average cover…
Comment: Software for Spatial Transcriptomic data [NanoString; Visium]?
by
LauferVA
3.8k
Other relevant posts are gathered here. I'll start sorting through these and redact an answer in a day or two if no more specific answer em…
Comment: Downsampling ATAC-seq BAM files
by
Elise
• 0
Single-nucleus as a part of the 10x multiomics protocol, yes.
Comment: Filling gaps in BAM file
by
seidel
11k
> By gaps, I think I mean just sections of the genome where there was not sufficient coverage or data to produce reliable reads for the BAM…
Comment: ANNOVAR Download Failing
by
Ram
41k
Please verify your internet connectivity using, say, `ping www.google.com`.
Answer: Calculate GC content for entire chromosome
by
ATpoint
78k
https://www.biostars.org/p/358684/#358687
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