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160 results • Page
2 of 4
Sort: Views
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Views
Votes
Replies
0
votes
2
replies
611
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
0
replies
605
views
Pan-genome Bioinformatics Workshops?
pan-genome
workshop
updated 13 hours ago by
Ram
39k • written 3.7 years ago by
cassondranewman
• 0
0
votes
0
replies
587
views
Proportion of traits in several groups
propotion-test
fishers-exact-test
updated 3 days ago by
Ram
39k • written 3.8 years ago by
biobiu
▴ 140
1
vote
1
reply
574
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 3 days ago by
GenoMax
129k • written 3 days ago by
Mohd
▴ 20
0
votes
7
replies
572
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 6 days ago by
Vincent Laufer
★ 2.9k • written 10 days ago by
Camilo Andres
▴ 30
0
votes
0
replies
535
views
Online courses/studies bioinformatics
online-study
learning
updated 3 days ago by
Ram
39k • written 3.8 years ago by
MAR
• 0
0
votes
2
replies
520
views
1-way-2-fold cross family analysis
cross-family-analysis
updated 5 days ago by
Ram
39k • written 3.8 years ago by
sinha.shriprakash
▴ 20
1
vote
2
replies
519
views
How to mine plant-inducible promoter (PIP) box from Xanthomonas genus genome?
assembly
gene
genome
next-gen
updated 11 hours ago by
Ram
39k • written 3.6 years ago by
Kumar
▴ 100
0
votes
0
replies
471
views
Do we still really need to remove the sequence (Protein or Genome) redundancy when using deep learning approaches to construct prediction models?
sequence-redundancy
updated 4 days ago by
Ram
39k • written 3.9 years ago by
kurdt325
• 0
0
votes
0
replies
459
views
Error running gene expression based ProTINA
ProTINA
Time-Series
gene-expression
updated 6 days ago by
Ram
39k • written 2.5 years ago by
Omics data mining
▴ 220
0
votes
0
replies
455
views
Normalizing multiple conditons all together
RMA
microarray
time-series
updated 6 days ago by
Ram
39k • written 2.6 years ago by
Raheleh
▴ 250
1
vote
0
replies
445
views
Using STAR SJ.out.tab file to identify novel ncRNAs
time-course
RNA-seq
ncRNA
STAR
updated 6 days ago by
Ram
39k • written 18 months ago by
jennifer.conrad84
▴ 10
2
votes
5
replies
416
views
Cutadapt error: too many parameters.
cutadapt
parallel
bash
6 days ago by
DanielEB_fisk
• 0
0
votes
5
replies
376
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 3 days ago by
Joe
21k • written 3 days ago by
gunala.nikhil
• 0
4
votes
4
replies
359
views
Segmentation fault Biopython pairwise alignment
biopython
alignment
updated 6 days ago by
Joe
21k • written 10 days ago by
antoine.fauchois92
▴ 20
0
votes
4
replies
348
views
What are recommended parameters for the local protein alignment ?
protein
alignment
1 day ago by
Alexander
▴ 70
0
votes
8
replies
342
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
2
votes
3
replies
327
views
Low mapping percentage
mapping
STAR
RNAseq
2 days ago by
Sib
▴ 40
0
votes
1
reply
322
views
How to quantification proteomics data
proteomics
updated 11 hours ago by
eqoa45
• 0 • written 19 months ago by
LeeLee
▴ 10
0
votes
3
replies
307
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2
align_stats
trinity
1 day ago by
eimanpharmacist
▴ 20
0
votes
0
replies
303
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
5 days ago by
Vincent Laufer
★ 2.9k
4
votes
4
replies
286
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 4 days ago by
ATpoint
72k • written 4 days ago by
bioinfo
▴ 80
0
votes
4
replies
273
views
Identification of genes involved in my pathway
KEGG
keggGet
4 days ago by
smanzano250800
• 0
0
votes
1
reply
254
views
Comparing loci across catalogs
Stacks
reference
alignment
RADseq
adegenet
updated 3 days ago by
rycro_c
• 0 • written 13 months ago by
Austin
• 0
0
votes
2
replies
249
views
Error in download library file in expression console software
expression
microarray
console
6 days ago by
Mohammad
• 0
2
votes
4
replies
237
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 5 days ago by
Ram
39k • written 5 days ago by
miguellarrazlopezdenovales
• 0
1
vote
0
replies
234
views
miRDeep2 installation showing "ln: failed to create symbolic link './randfold': File exists" error.
miRDeep2
updated 6 days ago by
Ram
39k • written 6 days ago by
Supernova
• 0
0
votes
2
replies
225
views
BCR/TCR analysis using target capture sequencing data
capture
ngs
TCR
BCR
6 days ago by
J.F.Jiang
▴ 900
0
votes
3
replies
225
views
Query qbout single cell sequencing
fastq
ScRNA
updated 6 days ago by
Ram
39k • written 8 days ago by
abbas.waseem.gcu
▴ 20
0
votes
2
replies
225
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
11 hours ago by
demoraesdiogo2017
▴ 90
2
votes
5
replies
218
views
Embryo transcriptome
database
transcriptome
SRA
updated 9 hours ago by
ATpoint
72k • written 17 hours ago by
firefox91
• 0
1
vote
3
replies
218
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 5 days ago by
GenoMax
129k • written 5 days ago by
mls
• 0
1
vote
2
replies
216
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 3 days ago by
thadjudkins2
• 0 • written 4 days ago by
herh
• 0
0
votes
3
replies
216
views
hardfilter error
bam
recall
3 days ago by
bestone
▴ 10
0
votes
5
replies
215
views
variant allelic fraction
vep
updated 45 minutes ago by
Pierre Lindenbaum
154k • written 1 day ago by
malm
• 0
1
vote
9
replies
209
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 9 hours ago by
Ram
39k • written 12 hours ago by
peavy
• 0
1
vote
3
replies
208
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 5 days ago by
NikhilP
▴ 20
1
vote
2
replies
207
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
4 days ago by
rheab1230
▴ 140
1
vote
2
replies
204
views
Combination of ROC CURVE
roccurve
R
AUC
1 day ago by
Maria17
▴ 20
0
votes
3
replies
203
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
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
194
views
Bed files of narrowPeak in ENCODE
ENCODE
updated 6 days ago by
Ram
39k • written 4 weeks ago by
younglin113
▴ 50
0
votes
3
replies
191
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
4 days ago by
Mohd
▴ 20
0
votes
1
reply
188
views
How to introduce normalized and scaled seurat data into monocle 3?
Monocle
scRNA-seq
Seurat
updated 6 days ago by
fracarb8
▴ 950 • written 8 days ago by
Sun
• 0
1
vote
3
replies
187
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 5 days ago by
Pierre Lindenbaum
154k • written 5 days ago by
herh
• 0
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 5 days ago by
linnet.roque6
▴ 10
1
vote
2
replies
180
views
sorting BAM file
BAM
updated 5 days ago by
ATpoint
72k • written 6 days ago by
Mohammad Amin
• 0
0
votes
3
replies
179
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
178
views
Different alternatives for downloading GWAS summary statistics en masse
GWAS
6 days ago by
Vincent Laufer
★ 2.9k
0
votes
1
reply
177
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 3 days ago by
raphael.B
▴ 360 • written 3 days ago by
sonsunjirachote
• 0
160 results • Page
2 of 4
Recent Votes
Contigs to chromosomes annotation
A: Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
A: Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
Comment: Help with running ATAC using Encode pipeline
Answer: Finding Enhancers using Genomation library
Comment: Is my estimated genome coverage correct?
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Recent Replies
Comment: Getting same value for start and end position, "DNA methylation"
by
ATpoint
72k
Yes, that is what methylkit is for. See my answer.
Comment: Italicise annotations with pheatmap
by
ATpoint
72k
Inkscape you learn in a day, for basic image and figure manipulation it's really simple and a good skill to have. Highly recommended.
Comment: Installation of PPFinder
by
subashini.fbtpb106
• 0
Can you suggest me any software that does gene prediction by masking pseudogenes?
Comment: variant allelic fraction
by
Pierre Lindenbaum
154k
IMHO this is like asking for the cow when you only have a steak :-)
Comment: Getting same value for start and end position, "DNA methylation"
by
Pankaj
• 0
yes I am working on Bisulphate sequenced data.
Answer: Get relationships and hierarchies for GO terms
by
rfran010
▴ 140
Maybe stringdb? seems to have an option to do what you describe. https://string-db.org/cgi/input?sessionId=bmYwdg48WePq&input_page_activ…
Comment: How to calculate TPM from featureCounts output
by
rfran010
▴ 140
This file is your counts file, isn't it?
Comment: Help with running ATAC using Encode pipeline
by
rfran010
▴ 140
Curious, can you give specific examples of what you refer to as "input file" and "json file"? In the screenshot you shared, input files re…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
rfran010
▴ 140
What version are you running? I use v2.0.3 on the command line. It looks like this option may be added in a later version, with `GTF.attrT…
Answer: Get relationships and hierarchies for GO terms
by
Vincent Laufer
★ 2.9k
Hey Daniel, **First, one potential caveat.** Above, you say "I have obtained several GO terms (indicating function and biological proc…
Comment: Perl. How to retrieve data until a keyword in GenBank?
by
Fungi-Beware!
▴ 10
THANK YOU!! Your method works!! And by removing: $data = ''; I figured out how to retrieve the annotation info with a prompt: …
Comment: variant allelic fraction
by
malm
• 0
Ok but i have only vep files i don't have vcf files
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data.
by
Yeeshouw
• 0
Yes, I am inputting a GTF file. I reviewed the `[featureCounts][1]` documentation, and I could not find this `extraAttributes` parameter. …
Comment: Italicise annotations with pheatmap
by
jamie.pike
▴ 80
@ATpoint Very true! I'm not so familiar with many image editing software and I wonder if it will be just as quick for me to try in R, but I…
Comment: Italicise annotations with pheatmap
by
jamie.pike
▴ 80
You're right, I was trying to save time and not write for in ComplexHeatmap, but using @Trivas ComplexHeatmap::pheatmap() should help! Than…
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