Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
1
view
Cross-strand correlation for paired-end ChIP-seq data
paired-end
ChIP-seq
RelCC
single-end
just now by
alison.ludzki
• 0
0
votes
0
replies
7
views
Long-read sequencing data simulation using CAMISIM
CAMISIM
20 minutes ago by
anna
• 0
0
votes
11
replies
204
views
I have encountered some bugs in transcriptome analysis using STAR and RSEM.
STAR
RSEM
updated 21 minutes ago by
GenoMax
145k • written 11 hours ago by
Pallondyle
• 0
0
votes
0
replies
30
views
Merging bfiles
merge
fam
plink
bfile
bed
3 hours ago by
aj123
▴ 120
0
votes
0
replies
43
views
Sankey + dot plot
ontology
R
sankey
GO
gene
6 hours ago by
Sofia
• 0
0
votes
0
replies
41
views
Visualizing Upregulated and Downregulated Genes in GO and KEGG Pathway Analyses
RNA-Seq
8 hours ago by
roxana
• 0
0
votes
0
replies
39
views
Issues with EnrichPathway Barplot in Reactome Pathway Analysis
RNA-Seq
8 hours ago by
roxana
• 0
0
votes
0
replies
49
views
VCF file missing MQRankSum and ReadPosRankSum for certain entries
snp
vcf
gatk
9 hours ago by
CRL-CHAR
• 0
0
votes
2
replies
149
views
Can't run CrossMap
CrossMap
15 hours ago by
Muhammad
• 0
0
votes
2
replies
122
views
ChromHMM bed file annotation
Chromhmm
annotation
20 hours ago by
SEJAL
• 0
0
votes
0
replies
70
views
Confusing Pathway Analysis Results from DAVID
DAVID
Reactome
KEGG
1 day ago by
saamhasan55
▴ 10
0
votes
0
replies
96
views
Can someone install me (remotely) Amber24?
Amber24
1 day ago by
Belén
• 0
0
votes
0
replies
91
views
ChromHMM
annotation
promoter
chromhmm
1 day ago by
SEJAL
• 0
0
votes
0
replies
84
views
Unable to analyse with cytoscape plugin bingo
Bingo
1 day ago by
bookorg
▴ 10
3
votes
4
replies
228
views
No available matched normal for Mutect2 GATK
GATK
1 day ago by
shems2001
• 0
0
votes
2
replies
260
views
Calculation of per-base average Quality (MAPQ, basecall quality Q20) from BAMs across multiple samples
MAPQ
BAM
coverage
1 day ago by
Novice
• 0
0
votes
0
replies
142
views
invalid class “DimReduc” object in `ArchR`
ArchR
2 days ago by
Dan
▴ 180
0
votes
1
reply
189
views
Extracting column from one seurat object based on common column and adding to the other object
R
SEURAT
updated 2 days ago by
bk11
★ 2.9k • written 2 days ago by
Varun Gupta
★ 1.3k
0
votes
0
replies
130
views
Pedigree information
pedigree
plink
king
2 days ago by
heureuse
• 0
0
votes
0
replies
136
views
Bandage visualization of the transcriptome
Trinity
transcriptomics
Bandage
RNA-seq
updated 2 days ago by
Ram
44k • written 2 days ago by
Lada
▴ 30
0
votes
0
replies
130
views
Can't merge snATAC samples
snATAC
2 days ago by
myoui3122010
▴ 20
0
votes
1
reply
525
views
PennCNV step1.1 error
xml
apt-probeset-genotype
PennCNV
CEL
APT
updated 2 days ago by
Volter
• 0 • written 15 months ago by
jaredgichohi
• 0
0
votes
0
replies
148
views
Pseudohaplotype assembly with Hifiasm and sex chromosomes from XY specimen
Hifiasm
3 days ago by
acarter
• 0
0
votes
0
replies
150
views
NeuronChat: identifyCommunicationPatterns_Neuron() error
R
NeuronChat
3 days ago by
sooni
▴ 20
0
votes
1
reply
204
views
Pre-imputation checks using 1000G data (hg19) for a hg38 VCF
preimputaitonCheck
updated 3 days ago by
bk11
★ 2.9k • written 3 days ago by
guoweidora
• 0
2
votes
2
replies
1.7k
views
Weird behaviour - WGCNA hub analysis results in Cytoscape through CytoHubba plugin change every time I run it!
rnaseq
wgcna
cytoscape
hubs
cytohubba
updated 3 days ago by
Ellie
• 0 • written 2.3 years ago by
Raito92
▴ 100
0
votes
0
replies
142
views
differential abundance of two groups using one sample in one of the groups
amplicon_sequencing
differential_abundance
picrust2
soil_microbiome
3 days ago by
michele.lamprillo
• 0
5
votes
7
replies
357
views
Genome Assembly Workflow assessment
flye
genome-assembly
pilon
racon
3 days ago by
Umer
▴ 110
0
votes
2
replies
211
views
SPAdes for specific strain assembly from stool sequenced data
assembly
SPAdes
fastq
3 days ago by
chemokine-1
▴ 10
0
votes
0
replies
150
views
metatranscriptome analysis pipeline
Metatranscriptome
3 days ago by
SHIRUI
• 0
1
vote
7
replies
554
views
cellranger count error:An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input
cellranger
1 day ago by
CRISPYCC
• 0
0
votes
7
replies
451
views
ncRNA, pseudogenes and lncRNA genes in highly variable features ( scRNA)
single-cell
updated 18 hours ago by
dsull
★ 6.8k • written 4 days ago by
carolofharvest
▴ 40
0
votes
3
replies
236
views
Grenedalf - error reads sam, bam, sync files
Grenedalf
pool-seq
updated 3 days ago by
GenoMax
145k • written 4 days ago by
Elizabeth
▴ 30
0
votes
0
replies
139
views
Keep seeing same degs everytime after filtering and clustering (scRNA)
single-cell
updated 4 days ago by
Ram
44k • written 4 days ago by
carolofharvest
▴ 40
0
votes
0
replies
146
views
Proxy Variant SNP for PRS
SNP
prs
proxy
updated 4 days ago by
zx8754
12k • written 4 days ago by
curious_butterfly
• 0
1
vote
8
replies
324
views
Beagle Gives Error no matter what i do
Beagle
Impute
SNPs
4 days ago by
Emilie
▴ 10
5
votes
6
replies
7.4k
views
GATK "We encountered a non-standard non-IUPAC base in the provided reference: '13"
GATK
updated 4 days ago by
GenoMax
145k • written 8.9 years ago by
Phismil
▴ 20
0
votes
0
replies
131
views
Hi-C Data and RNA-seq in a Non-Cell-Specific Context (Human Blood)
RNAexpression
interactions
repeats
Hi-C
4 days ago by
Smriti
▴ 30
1
vote
1
reply
199
views
Interpreting MA plot - DEG
R
DEG
ggplot2
updated 4 days ago by
Ram
44k • written 5 days ago by
NEWBIE
• 0
0
votes
0
replies
144
views
Masking LCR and PARs for GATK GermlineCNVCaller
GermlineCNVCaller
PAR
LowMappabilityRegions
GATK
CNV
5 days ago by
Maverick
▴ 10
2
votes
1
reply
623
views
Understanding behaviour of SCTransform in Seurat
Seurat
scRNASeq
normalization
updated 5 days ago by
alg507
• 0 • written 4 months ago by
yura.grabovska
▴ 430
0
votes
0
replies
175
views
Missing value where TRUE/FALSE needed in Seurat's IntegrateLayers(), unsure if error with Seurat or session
seurat
5 days ago by
K
• 0
0
votes
0
replies
134
views
Significant colocalisation across two GWAS SumStats with opposite "effect sizes"
coloc
effect-size
GWAS
colocalisation
5 days ago by
Pine
▴ 20
0
votes
0
replies
118
views
How to interpret a probability equal to 1 in TargetNet web service?
models
Drug-target-interaction
SAR
TargetNet
updated 5 days ago by
Ram
44k • written 5 days ago by
clara-28
• 0
1
vote
1
reply
170
views
Samtools: exclude secondary and supplementary alignments
samtools
updated 5 days ago by
Ram
44k • written 5 days ago by
Alexandra
• 0
0
votes
0
replies
136
views
generate consensus sequence for PSMC analysis
bcftools
consensus-sequence
updated 6 days ago by
Ram
44k • written 6 days ago by
asatullayevtemurrr
• 0
0
votes
2
replies
220
views
Tools for assembling Plasmid Genome
Illumina
Plasmid
E.coli
Assembly
5 days ago by
adarsh_munna
▴ 50
1
vote
4
replies
304
views
Poor dispersion fit in DESeq2
deseq2
RNA-seq
edgeR
limma
updated 6 days ago by
Ram
44k • written 6 days ago by
Ben
▴ 20
1
vote
5
replies
354
views
RNASeq Analysis: data from different library
RNA-seq
ngs
updated 6 days ago by
i.sudbery
20k • written 6 days ago by
Matteo
• 0
0
votes
4
replies
290
views
R-studio, install, R, Installation error
Rstudio
offtopic
updated 4 days ago by
Michael
55k • written 6 days ago by
naveennavinbeast
• 0
1,000 results • Page
1 of 20
Recent Votes
Answer: How to compile Multiz
Answer: Difference between GLM and Wilcoxon rank sum test
Answer: MarkDuplicatesSpark GATK flags for overcoming space issues
Answer: Numreads from samtools for Differential Expression
Comment: Numreads from samtools for Differential Expression
Answer: How to compile Multiz
C: How to make an intronic GTF for alignment
Recent Locations •
All
India,
3 minutes ago
United States,
4 minutes ago
United States,
11 minutes ago
China,
14 minutes ago
Hong Kong,
15 minutes ago
United States,
22 minutes ago
Japan,
26 minutes ago
Recent Awards •
All
Scholar
to
Mimi33
▴ 10
Popular Question
to
KatharinaKopp
• 0
Popular Question
to
CRL-CHAR
• 0
Scholar
to
Jaber
• 0
Teacher
to
tothepoint
▴ 930
Popular Question
to
bookorg
▴ 10
Popular Question
to
dpc
▴ 250
Recent Replies
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
https://www.biostars.org/u/145859/ : Use `ADD REPLY/ADD COMMENT` to add additional information to existing threads. `ADD YOUR ANSWER` is me…
Comment: How to compile Multiz
by
GenoMax
145k
Please do not ask questions unrelated to the original post in this thread. Post a new question.
Comment: How to compile Multiz
by
Santex
• 0
I could install multiz from it! Thank you very much. Please help me out with the problem below. I run multiz like below. (myenv) tak…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
One of them looks okay, but I don't quite believe it. ```R > table(df$`intermediate_data.OE1_1_.genes.results`==0) FALSE TRUE 21200 2…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
It seems that the files that generated the results also have significant issues. Except for one sample, all other samples only have over 20…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
Their .fq files all look similar, should I rerun these programs?
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
GenoMax
145k
> Cannot open intermediate_data/OE_NC_2_.temp/OE_NC_2__alignable_1.fq! It may not exist. Looks like you are missing some files. BTW this …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
The most torturous thing is that some groups did indeed generate results. ``` ls intermediate_data KO1_1_.stat KO1_3_.isoforms…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
However, OE1_2 and OE1_3 are not the only groups experiencing problems. I tried another non-empty file, and: ``` rsem-calculate-expression …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM.
by
Pallondyle
• 0
oops ``` file *.out.bam KO1_2Aligned.sortedByCoord.out.bam: gzip compressed data, extra field KO1_2Aligned.toTranscriptome.out.bam: …
Answer: Converting bam to sam using htslib C++ api
by
Pierre Lindenbaum
164k
read https://github.com/samtools/samtools/blob/develop/sam_view.c * allocate a new bam1_t* b = bam_init1 * open the input file: sam_op…
Comment: Converting bam to sam using htslib C++ api
by
Pierre Lindenbaum
164k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: FastQC and HISAT2
by
Jaber
• 0
Thank you, it worked almost after two months of struggle, I nearly deleted everything and reinstalled it, I assume the problem was someth…
Traffic: 1273 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6