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352 results • Page
4 of 8
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
157
views
admixfrog for high-coverage data
introgression
13 days ago by
gubrins
▴ 290
0
votes
1
reply
236
views
updateR() error
R
update
updated 10 days ago by
dthorbur
★ 1.7k • written 13 days ago by
marco.barr
▴ 30
0
votes
0
replies
163
views
Haplotype Phasing from Yeast strains
yeast
haplotype
phasing
13 days ago by
Sven K
• 0
0
votes
0
replies
171
views
cufflinks- cuffquant issue
cufflinks
14 days ago by
soyeon
• 0
2
votes
2
replies
263
views
compare dimplot(single cell)
DEG
scRNAseq
13 days ago by
kayah
• 0
1
vote
1
reply
236
views
--busco_db and --busco_seed_species with RNA-seq
RNA-seq
Funannotate
busco
14 days ago by
sansan_96
▴ 50
0
votes
0
replies
163
views
Computational Package to engage Type 2 Diabetes Knowledge Portal (T2DKP)
workflow
Package
14 days ago by
Shicheng Guo
★ 9.4k
0
votes
1
reply
200
views
Pathway activity in Bulk-RNA-SEQ analysis
R
RNA-seq
transcriptomics
updated 14 days ago by
jared.andrews07
★ 16k • written 14 days ago by
PBC
▴ 10
1
vote
1
reply
208
views
lncRNA and ncPEPs identification
lncRNA
updated 14 days ago by
Yahel
• 0 • written 15 days ago by
atharvakarkare14
▴ 10
0
votes
0
replies
128
views
Music2 human to mouse deconvolution
deconvolution
liftover
music2
14 days ago by
rbronste
▴ 420
0
votes
2
replies
200
views
Weird Basecalled reads PHRED quality plot from pycoQC
pycoQC
nanopore
sequencing
14 days ago by
njornet
▴ 10
0
votes
0
replies
136
views
computeGCBias outputs
GC
bam
deepTools
GCbias
14 days ago by
pablo
▴ 300
0
votes
0
replies
116
views
Pindel zygosity determination
depth
vaf
pindel
Zygosity
14 days ago by
arya.sagittarius
▴ 10
1
vote
3
replies
232
views
How to predict the affinity between Protein and RNA?
Protein-RNAinteractions
prediction
deeplearning
updated 10 days ago by
dthorbur
★ 1.7k • written 14 days ago by
Alex
• 0
2
votes
2
replies
214
views
Seeking Help with Cell Ranger Multi Error in fixed-RNA-profiling
chromium
fixed-RNA-profiling
cellranger
updated 7 days ago by
naveau
• 0 • written 14 days ago by
lam
▴ 10
0
votes
3
replies
240
views
data background noise
noise
data
updated 8 days ago by
dthorbur
★ 1.7k • written 14 days ago by
marco.barr
▴ 30
4
votes
6
replies
291
views
Protein loops
protein
Loop
14 days ago by
Curious
▴ 10
0
votes
0
replies
510
views
Looking for guidance on Microbial Association Networks (MANs) Inference with samples from different metagenomics/metatranscriptomics studies
microbialassociationnetworks
metatranscriptomics
metagenomics
netowrkbiology
14 days ago by
sebasar1245
• 0
0
votes
1
reply
127
views
Bed file
bedfile
updated 14 days ago by
Pierre Lindenbaum
160k • written 14 days ago by
Jeet
• 0
0
votes
0
replies
86
views
How can validate hub genes or significant factors using area under the ROC curve (AUC)?
R
AUC
genes
hub
validation
14 days ago by
wyt1995
▴ 30
0
votes
0
replies
93
views
Toxinpred 3.0 tool
peptide
protein
toxin
toxicity
updated 14 days ago by
zx8754
11k • written 14 days ago by
Saurabh
• 0
0
votes
3
replies
226
views
Microarray pbrobe ID to gene ID problem
microarray
updated 13 days ago by
GenoMax
140k • written 15 days ago by
mnx0723
• 0
0
votes
0
replies
99
views
Polysome profiling data
Polysome
updated 14 days ago by
Ram
43k • written 15 days ago by
Hasan_Daaboul
• 0
0
votes
0
replies
113
views
What to do with multiple genes in ballgown?
STAR
ballgown
DESeq2
15 days ago by
markusz
▴ 10
1
vote
9
replies
441
views
miRNA alignment with Bowtie2
bowtie2
13 days ago by
Chironex
▴ 40
0
votes
0
replies
94
views
Difference between reading concatenated PE reads into jellyfish and merging paired end .jf outputs independently
Jellyfish
Kmer
GenomeScope
15 days ago by
joshua.j.wright
▴ 10
0
votes
0
replies
109
views
ImmuCellAI
RStudio
ImmuCellAI
updated 15 days ago by
Ram
43k • written 15 days ago by
sana
• 0
0
votes
2
replies
202
views
Is there a program that can predict the sequence of an organisms telomeres just from raw sequencing reads
telomeres
genomics
sequencing
15 days ago by
Mark
• 0
0
votes
1
reply
133
views
Calculating (Groupwise) Log2fold change using values obtained from SST-RMA?
SST-RMA
genes
TAC
thermofisher
foldchange
updated 15 days ago by
ATpoint
81k • written 15 days ago by
purple909
• 0
0
votes
0
replies
107
views
Issue to run gatk4 spark
gatk
spark
15 days ago by
Mojtaba
• 0
2
votes
5
replies
608
views
I am trying to generate a bcf file through samtools mpileup but it taking too long, how long does it usually take to generate a bcf file?
alignment
sam
Bam
samtools
Bioinformatics
updated 14 days ago by
jkbonfield
★ 1.2k • written 15 days ago by
K
• 0
0
votes
1
reply
154
views
SNP and Genes position matching dataframes in R
R
dataframe
updated 15 days ago by
dthorbur
★ 1.7k • written 15 days ago by
QX
• 0
0
votes
1
reply
163
views
Alignment tool of repeat expansion detection
STR
NGS
readexpansion
updated 15 days ago by
Jesse
▴ 740 • written 16 days ago by
adarsh_pp
▴ 40
2
votes
7
replies
525
views
Does removal of contaminants in RNAseq data have an impact on downstream analyses?
RNA-seq
contamination
updated 15 days ago by
Chris Dean
▴ 390 • written 16 days ago by
ev97
▴ 20
0
votes
0
replies
130
views
HADDOCK 2.4
Protein
Docking
16 days ago by
Preeti
• 0
1
vote
5
replies
257
views
how to convert SummarizedExperiment files to DESeqDataSet??
scRNA-seq
DEG
DESeq2
updated 16 days ago by
Haci
▴ 550 • written 16 days ago by
kayah
• 0
1
vote
3
replies
288
views
FastQC on nanopore data: high proportion of polyA and polyG. Why ?
fastQC
polyG
ONT
nanopore
polyA
updated 16 days ago by
GenoMax
140k • written 16 days ago by
Matt
• 0
0
votes
0
replies
112
views
SAMstat mapping quality report MAPQ gt vs MAPQ lt
Sequencing
mapping
samstat
16 days ago by
njornet
▴ 10
3
votes
3
replies
408
views
I can't add VAF from population for all of my variants from VCF file
genomics
vcf
gnomad
updated 16 days ago by
Ram
43k • written 17 days ago by
Samuel
▴ 20
1
vote
4
replies
269
views
Some questions about bulk RNA-seq data normalization
RNA-seq
NGS
bulk
normalize
16 days ago by
feather-W
• 0
2
votes
4
replies
258
views
repeatseq compilation issues
NGS
Repeats
repeatseq
repeatexpansion
Genomics
updated 16 days ago by
Michael
54k • written 17 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
113
views
ComplexHeatmap anno_mark position changes with height of gene expression heatmap
ComplexHeatmap
17 days ago by
CTLong
▴ 90
0
votes
0
replies
113
views
compare the assembler MaSuRCA and SPAdes for assembly unmapped reads
SPAdes
unmapped_reads.
assembly.
MaSuRCA.
17 days ago by
Sony
▴ 10
0
votes
0
replies
119
views
MG-RAST KEGG KO Search
mg-rast
kegg
metagenomics
ko
17 days ago by
Jeremy
▴ 880
0
votes
5
replies
392
views
Same NCBI IDs for different Ensembl IDs / Multiple NCBI IDs for an Ensembl ID
KEGG
ENTREZ
ENSEMBL
16 days ago by
Maxwell
▴ 20
1
vote
9
replies
802
views
Python3 or Ubuntu, not perl: Have Primers with Degenerate Bases, Need tool or way to List all Possible Nucleotide Sequences
degenerate-bases
python
primers
biopython
updated 16 days ago by
Dave Carlson
★ 1.7k • written 17 days ago by
Matthew
• 0
0
votes
1
reply
147
views
Snakemake wrapper issue
fastqc
snakemake
updated 17 days ago by
Ram
43k • written 17 days ago by
Matvii Mykhailichenko
• 0
0
votes
0
replies
99
views
MIRA runs yielding different assemblies with same input data and parameters
MIRA
replication
denovo
assembly
17 days ago by
btc347
• 0
0
votes
1
reply
152
views
Understanding Uncommon Genotype Formats in VCF Files Generated by nf-core RNAvar Pipeline
genotype
rnaseq
updated 17 days ago by
Pierre Lindenbaum
160k • written 17 days ago by
ASid
▴ 40
2
votes
2
replies
212
views
ggplot2 installation
ggplot2
updated 17 days ago by
rpolicastro
13k • written 17 days ago by
safeassli
• 0
352 results • Page
4 of 8
Recent Votes
Comment: Gene reads all zero for each sample
Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Recent Awards •
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Teacher
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Pierre Lindenbaum
160k
Popular Question
to
brian.fristensky
▴ 460
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Ann
★ 2.4k
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140k
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104k
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amitpande74
▴ 20
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beacamara
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Recent Replies
Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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