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88 results • Page
2 of 2
Sort: replies
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Views
Votes
Replies
1
vote
1
reply
453
views
How is the best way to filter a BED file to get specific exons from their gene ID
bed
updated 9 hours ago by
Ram
38k • written 10 months ago by
ManuelDB
▴ 30
0
votes
1
reply
277
views
exome targeted regions ensembl
bed
exome
updated 8 hours ago by
Ram
38k • written 12 months ago by
mailard
▴ 10
1
vote
1
reply
3.3k
views
How do I find cross-reactive species given two primers?
primer
blast
updated 8 hours ago by
Ram
38k • written 7.8 years ago by
andytsaica
• 0
0
votes
1
reply
301
views
Assign RSID to ID . / blank column in vcf file
ID
VCF
updated 8 hours ago by
Ram
38k • written 13 months ago by
Nai
▴ 50
0
votes
1
reply
77
views
ClusterProfiler enrichKEGG – remove organism name in plots?
KEGG
ggplot2
enrichKEGG
ClusterProfiler
updated 7 hours ago by
Mensur Dlakic
★ 23k • written 7 hours ago by
Sian
• 0
0
votes
1
reply
149
views
mrbayes segmentation fault
mrbayes
segmentation
fault
updated 23 hours ago by
Mensur Dlakic
★ 23k • written 1 day ago by
dgrace999
• 0
0
votes
0
replies
170
views
Save Scene File in PDB in YASARA
YASARA
SCENE
PDB
updated 10 hours ago by
Ram
38k • written 9 months ago by
misbahnaseem95
• 0
0
votes
0
replies
187
views
How to convert .bed/.bim/.fam file to .dat file to run --dosage command to get INFO
plink
dosage
updated 10 hours ago by
Ram
38k • written 9 months ago by
Raju
• 0
0
votes
0
replies
424
views
Measure genome-wide agreement of peaks in
bigwig
atac-seq
macs2
updated 13 hours ago by
Ram
38k • written 17 months ago by
Al Murphy
▴ 30
0
votes
0
replies
505
views
Error in genetics vcf file - !! Error (genfile::MalformedInputError): Source "file-path/data_chrxx.vcf.gz" is malformed on line 5145934..
vcf
genetics
updated 8 hours ago by
Ram
38k • written 15 months ago by
Nance
• 0
0
votes
0
replies
54
views
Error when using compareCluster from enichment
compareCluster
13 hours ago by
jacob
• 0
0
votes
0
replies
266
views
how can I extract RNA expression from Klein dataset
single-cell
RNA
expression
updated 14 hours ago by
Ram
38k • written 16 months ago by
poria.laghayee
• 0
0
votes
0
replies
156
views
How to generate a bed file indicating increased ratio of H3K4me3 to H3K4me1
H3K4me3
bed
H3K4me1
updated 9 hours ago by
Ram
38k • written 10 months ago by
jia
• 0
0
votes
0
replies
163
views
MEME motif discovery
fasta
updated 9 hours ago by
Ram
38k • written 10 months ago by
kaisakaiho73847
• 0
0
votes
0
replies
89
views
Quality control of the X-chromosome for use in a GWAS using REGENIE
REGENIE
GWAS
LMM
chromosome-X
quality-control
19 hours ago by
ucbtep
▴ 20
0
votes
0
replies
597
views
what is the effective population size in a plot from psmc software?
demography
genome
psmc
gene
updated 14 hours ago by
Ram
38k • written 2.3 years ago by
a4appy23
▴ 50
0
votes
0
replies
225
views
Tapestry scDNA-seq and translocations
scDNA-seq
H5
single-cell
MOSAIC
variant-calling
updated 9 hours ago by
Ram
38k • written 11 months ago by
jmnz22
• 0
0
votes
0
replies
217
views
Merging Sample in vcf file having SNPs info
VCF
updated 9 hours ago by
Ram
38k • written 11 months ago by
amar.kant20422
• 0
0
votes
0
replies
540
views
gene expres. simulation with R
rnorm
simulation
R
updated 14 hours ago by
Ram
38k • written 2.3 years ago by
bioinfonewbie
• 0
0
votes
0
replies
477
views
Find conditions where target gene is most differentially expressed (CBioPortal/TCGA)
tcga
cbioportal
updated 14 hours ago by
Ram
38k • written 2.3 years ago by
Dirk
▴ 100
0
votes
0
replies
510
views
Problem with MIREAP microRNA detection in larger libraries
mireap
small-RNA
microRNA
RNA-Seq
updated 15 hours ago by
Ram
38k • written 2.2 years ago by
lauren.todd
• 0
0
votes
0
replies
487
views
Target genes of lncRNAs
Cufflinks
RNA-Seq
lncRNAs
updated 15 hours ago by
Ram
38k • written 2.2 years ago by
Reza
• 0
1
vote
0
replies
78
views
Creating sample groups from a combination of genes for survival analysis
Survival
7 hours ago by
krushnach80
★ 1.1k
0
votes
0
replies
79
views
How to shift the position of multiallelic variants for phasing analysis with SHAPEIT2?
NGS
bcftools
vcf
phase
17 hours ago by
zhangfish
▴ 40
0
votes
0
replies
116
views
Dnaplotter
Artemis
21 hours ago by
prs
• 0
0
votes
0
replies
34
views
inquiry related to Hi-C data download
Hi-C
datasets
human
brain-cortex
interaction
matrix
4 hours ago by
rheab1230
▴ 140
0
votes
0
replies
182
views
Diffbind output file default contrasts
Diffbind
updated 8 hours ago by
Ram
38k • written 13 months ago by
c.eskiw
▴ 10
0
votes
0
replies
67
views
Homer annotatePeaks for enrichment analysis
annotatePeaks
homer
DMR
methylation
17 hours ago by
Joana
• 0
0
votes
0
replies
102
views
Seurat analysis without ribosomal genes
single-cell
transcriptomics
seurat
18 hours ago by
firestar
★ 1.5k
0
votes
0
replies
87
views
Add HI:i:<n> tag to a BAM file
SAM
hisat2
STAR
tag
BAM
18 hours ago by
predeus
★ 1.8k
0
votes
0
replies
71
views
Need Help Scraping MeSH terms from Pubmed
Python
Entrez
Scraping
updated 13 hours ago by
Ram
38k • written 14 hours ago by
Arnau
• 0
0
votes
0
replies
455
views
How to plot heatmap for the matrix for the pairwise comparison of sequence similarity in python?
heatmap
python
distance-matrix
updated 8 hours ago by
Ram
38k • written 15 months ago by
ramsha
• 0
0
votes
0
replies
188
views
PSL file confusion on negative strand
BLAT
PSL
updated 10 hours ago by
Ram
38k • written 8 months ago by
spark
• 0
0
votes
0
replies
187
views
Comparing PopoolationTE2 output with reference .bed file in Python
bed
python
pandas
PopoolationTE2
updated 10 hours ago by
Ram
38k • written 8 months ago by
Emilia
• 0
0
votes
0
replies
375
views
Using infercnv R package
r
infercnv
Seurat
annotation
updated 13 hours ago by
Ram
38k • written 6 months ago by
j.jacob1
• 0
0
votes
0
replies
274
views
SURVIVOR bed file
BED
CNV
SURVIVOR
VCF
updated 10 hours ago by
Ram
38k • written 8 months ago by
Nameless
• 0
0
votes
0
replies
337
views
Validation of Bioinformatics pipeline with NA12763
hap.py
updated 13 hours ago by
Ram
38k • written 23 months ago by
esimonova.me
▴ 20
0
votes
0
replies
67
views
OrthoFinder problem
Sub
OrthoFinder
iterative
processes
Bash
13 hours ago by
HERMAN
▴ 10
88 results • Page
2 of 2
Recent Votes
Answer: RNA-SEQ
Comment: RNA-SEQ
Comment: RNA-SEQ
Answer: RNA-SEQ
Gene Set Enrichment Analysis
Can I sort my bam files with Picard MergeSamFiles?
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
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Answer: activity of unloaded/unassembled Tn5
by
callumjcparr
• 0
So I hope someone is still interested in this. We have taken to preparing recombinant Tn5 now as it's much cheaper than commercial supp…
Comment: RNA-SEQ
by
ali
• 0
thanks for your helping
Comment: TSS of protein coding genes
by
ConvolutedGenome
▴ 10
I am quite confused with GENCODE GTF file, So, within the GENCODE GTF file, I noticed that each (protein-coding) gene has multiple "transc…
Comment: Recommendation for (Alternative) Splicing analysis packages for bulk RNA-seq da
by
iraun
5.8k
Hi! I personally use [SplAdder][1], in case you want to add it to your list :). [1]: https://github.com/ratschlab/spladder
Answer: Problem generating a .vcf after upgrade of samtools and bcftools
by
Andy
• 0
Really the only needed, that help worked, thank's
Comment: Active enhancers for mm39
by
seidel
11k
Just curious what you mean by "active" enhancers. Enhancers are active in a given context (e.g. cell type developmental state, etc.), and m…
Comment: Creating loop for read groups using Picard
by
ntsopoul
▴ 20
try absolute paths navigate to the directory with cd and use pwd to get the absolute directory.
Comment: how to create interacting Hi-C peaks
by
rheab1230
▴ 140
Thank you. I will use this package since I am more familiar with R
Comment: how to create interacting Hi-C peaks
by
rheab1230
▴ 140
thank you. i will go through it
Comment: Fastqc report analysis
by
npavliukovec
• 0
Yeah, after trimming and fastqc I will have to generate MultiQC plots and after do mapping with reference genome. As I know, for eukaryotes…
Comment: My fastq files(paired end) have different read number
by
kimgeng
• 0
Oh, I see, Thank you however, I want to make vcf files with gatk haplotypecaller and GenotypeGVCFs. But I got some problems I have about 2.…
Answer: My fastq files(paired end) have different read number
by
ntsopoul
▴ 20
Yes, this is normal because depending on how you generate the bam file, the non-aligning reads are saved in the .bam file along the properl…
Answer: Can I use abundance from Tximport to compare the expression level of transcript
by
ntsopoul
▴ 20
No, you should not do that since the count matrix is not normalized. Also, the statistics for getting a pValue requires consideration of al…
Comment: Easy way to split VCF file by chromosome
by
Joana
• 0
You need to run bcftools index on your vcf file before running the suggested command.
Comment: Fastqc report analysis
by
ntsopoul
▴ 20
I think you are fine, no worries. Will you go ahead an align the fastq files to a genome? Do you know how?
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