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1,000 results • Page
3 of 20
Sort: replies
Rank
Views
Votes
Replies
2
votes
9
replies
7.5k
views
6 follow
Read MAP and PED files in PLINK
GWAS
PLINK
updated 4 months ago by
GenoMax
141k • written 6.0 years ago by
ft821525
• 0
1
vote
9
replies
1.0k
views
gene annotation
gtf
gene-annotation
updated 11 months ago by
Ram
43k • written 11 months ago by
ahmad
• 0
0
votes
9
replies
474
views
Low number of both surviving reads after trimming
trimmomatic
trimming
25 days ago by
Jay
• 0
0
votes
9
replies
5.4k
views
Calculating FPKM and TPM by hand from htseq-count output?
RNA-Seq
rna-seq
htseq
FPKM
TPM
updated 8 months ago by
ATpoint
81k • written 5.0 years ago by
Joel Wallenius
▴ 210
2
votes
9
replies
1.1k
views
Read length for single -ended RNA seq data analysis
read-length
fastq
updated 8 months ago by
Ram
43k • written 8 months ago by
vinaya
• 0
4
votes
9
replies
1.2k
views
Snakemake issue with wrappers
Python
Snakemake
5 months ago by
Begonia_pavonina
▴ 150
1
vote
9
replies
1.2k
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 10 months ago by
Ram
43k • written 10 months ago by
peavy
• 0
0
votes
9
replies
753
views
how to use multiple command in one line with using the output of last command to the next
bedtools
linux
bed
4 months ago by
sata72
• 0
3
votes
9
replies
780
views
Understanding this analysis pipeline
reads
updated 9 months ago by
Ram
43k • written 9 months ago by
artemchuki
• 0
4
votes
9
replies
994
views
bcl2fastq troubleshooting all reads dumped to "Undetermined"
demultiplex
illumina
sequencing
updated 4 months ago by
GenoMax
141k • written 4 months ago by
MaxF
▴ 120
0
votes
9
replies
975
views
gene id
gene-id
NCBI
updated 9 months ago by
GenoMax
141k • written 10 months ago by
safeassli
• 0
3
votes
9
replies
971
views
Estimate sizes of repeats in a especific Gene
CGG
Fragile-X
11 months ago by
Rafael
▴ 10
4
votes
9
replies
561
views
variant calling
variant-calling
updated 19 days ago by
Ram
43k • written 20 days ago by
dalibenam64
• 0
6
votes
9
replies
2.0k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM
Bowtie
updated 11 months ago by
Ram
43k • written 15 months ago by
luzglongoria
▴ 50
2
votes
9
replies
1.2k
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
4 months ago by
ian.will
▴ 30
1
vote
9
replies
517
views
miRNA alignment with Bowtie2
bowtie2
5 weeks ago by
Chironex
▴ 40
1
vote
9
replies
848
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 5 weeks ago by
Dave Carlson
★ 1.7k • written 6 weeks ago by
Matthew
• 0
3
votes
9
replies
1.7k
views
How to get negative training set if I don't know what constitutes negative?
machine-learning
dna-sequence
blast
updated 5 months ago by
Ram
43k • written 7.6 years ago by
nafizh
• 0
1
vote
9
replies
1.5k
views
blast retrieves "N/A" for taxonomic data
blast
blastn
updated 6 weeks ago by
flavianegrete
• 0 • written 3.4 years ago by
langziv
▴ 50
1
vote
9
replies
2.1k
views
kallisto bootstrap / condo installation problem
hfd5
kallisto
condo
updated 12 months ago by
dsull
★ 5.8k • written 12 months ago by
micecanfly
▴ 10
1
vote
9
replies
870
views
Command line or python RNA-seq read simulator
simulation
RNA-seq
5 months ago by
i.sudbery
19k
0
votes
9
replies
1.2k
views
Normalization across different single cell RNAseq experimetns
global-scaling
single-cell
scRNA-seq
batch-effect
updated 6 days ago by
Ram
43k • written 3.9 years ago by
jmah
▴ 20
0
votes
9
replies
1.4k
views
Samtools sam to bam error
samtools
updated 5 months ago by
Andrea
• 0 • written 24 months ago by
kb_93
▴ 10
1
vote
9
replies
3.3k
views
build databses for genome using snpEff
annotation
SNP
snpEff
updated 8 months ago by
nehakhilwani18
• 0 • written 5.7 years ago by
StudentBio
• 0
0
votes
9
replies
893
views
fragments file generation via Sinto from CellRanger output
scATAC
alignment
scRNA
Sinto
10x
6 months ago by
ntsopoul
▴ 60
0
votes
9
replies
1.1k
views
grep multiple lines form file
shell-script
grep
updated 10 months ago by
Ram
43k • written 3.9 years ago by
harry
▴ 30
7
votes
9
replies
1.1k
views
Calculation of TMB on gene level
genomics
updated 6 months ago by
svp
▴ 680 • written 7 months ago by
smrutimayipanda
▴ 20
3
votes
8
replies
905
views
Can these RNAseq runs be combined?
transcriptomics
replicates
RNAseq
updated 10 months ago by
GenoMax
141k • written 10 months ago by
mdrnao
• 0
0
votes
8
replies
9.9k
views
how to find a read by name in a bam file
next-gen-sequencing
updated 10 months ago by
Ram
43k • written 6.8 years ago by
himanimalhotra89
• 0
1
vote
8
replies
811
views
DESEQ2 design in DESeqDataSetFromMatrix: cell and treatment
rna-seq
deseq2
5 months ago by
pingu77
▴ 20
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq
deseq2
updated 10 months ago by
Ram
43k • written 3.9 years ago by
kand3e
▴ 60
2
votes
8
replies
679
views
TCGA Biospecimens Slides Extraction
tcga
updated 8 weeks ago by
Zhenyu Zhang
★ 1.2k • written 9 weeks ago by
jain72744
▴ 10
0
votes
8
replies
4.4k
views
Downloading single cell data from NCBI
ncbi
rna-seq
fastq-dump
single-cell
updated 8 months ago by
Ram
43k • written 5.3 years ago by
V
▴ 380
1
vote
8
replies
3.9k
views
No gene can be mapped
R
GSEA
updated 4 months ago by
jv
★ 1.8k • written 2.3 years ago by
yang.zhizhang
• 0
1
vote
8
replies
1.2k
views
Betacoronavirus.00.nsq error
biostars-handbook
corona
updated 10 months ago by
Ram
43k • written 2.3 years ago by
Sam
• 0
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression
RNA-seq
gene-ontology
updated 13 days ago by
Ram
43k • written 6.5 years ago by
firestar
★ 1.6k
1
vote
8
replies
2.4k
views
subset data problem
R
seurat
8 months ago by
Andy
▴ 120
2
votes
8
replies
957
views
HGVS Nomenclature of Multiple Indels found in Cis
Nomenclature
HGVS
updated 8 weeks ago by
bharata1803
▴ 560 • written 4 months ago by
LauferVA
4.2k
0
votes
8
replies
997
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 10 months ago by
GenoMax
141k • written 10 months ago by
Marta
• 0
0
votes
8
replies
1.9k
views
Chromosome Location of Sequence in Fasta File using Biopython
biopython
python
updated 10 months ago by
Ram
43k • written 4.4 years ago by
muhammad.khizerkiet
• 0
1
vote
8
replies
963
views
Reads in IGV are mostly in intron regions
Patchseq
RNA-seq
10 months ago by
Kai_Qi
▴ 130
5
votes
8
replies
1.9k
views
looking for tools to detect RNA contamination in DNA
RNA-Seq
DNA-Seq
contamination
QC
updated 6 months ago by
Jingjingzhang
• 0 • written 3.7 years ago by
from the mountains
▴ 230
0
votes
8
replies
1.3k
views
Creating fastq subsets from existing files
scRNA-seq
umi_tools
cellranger
fastq
8 months ago by
Zack
• 0
1
vote
8
replies
2.5k
views
Using NCBIs EDirect to download pubmed abstract
edirect
pubmed
NCBI
updated 10 months ago by
Ram
43k • written 5.8 years ago by
zorn21g
• 0
1
vote
8
replies
1.4k
views
Same correlation values obtained at different soft threshold powers in WGCNA signed network analysis
sft
wgcna
langfelder
12 months ago by
Aditi
• 0
0
votes
8
replies
637
views
Phobius error: Could not read provided fasta sequence at phobius.pl line 408
Phobius
updated 7 weeks ago by
ido.idobar
▴ 10 • written 3 months ago by
Elizabeth
▴ 30
1
vote
8
replies
1.4k
views
counts of cite-seq-count vs. cellrenager varies tremendously
citeseq-count
cellranger
cite-seq
scRNA-seq
updated 4 months ago by
ATpoint
81k • written 9 months ago by
Assa Yeroslaviz
★ 1.8k
3
votes
8
replies
970
views
Single read sequence from a .fasta file cannot be aligned/BLASTN-d to my reference
BLAST
bowtie2
BWA
alignment
8 months ago by
cheesefish21
▴ 10
2
votes
8
replies
1.0k
views
VCF file CSQ flag
vcf
exome-sequencing
updated 10 months ago by
Ram
43k • written 10 months ago by
Payal
▴ 160
7
votes
8
replies
8.9k
views
Determining read count
trimmomatic
rna-seq
trinity
updated 8 months ago by
Ram
43k • written 8.0 years ago by
nikelle.petrillo
▴ 110
1,000 results • Page
3 of 20
Recent Votes
Comment: Correlation for ATAC-Seq and Chip-Seq
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Comment: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
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Answer: Plots for DNA methylation data
by
Basti
★ 2.0k
Yes you can use ggplot2 to create your own plots from a table of results from a differential methylation analysis. You just need to adapt a…
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by
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This forum is not dedicated to this type of request, there are many online tutorials for creating heatmaps accessible with simple internet …
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Download the CPC2 tool supported by python 3 from here [https://github.com/gao-lab/CPC2_standalone/releases/tag/v1.0.1][1]. Then follow …
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4.2k
let me know the scope and scale of the request (e.g. I need to do this for every record in Pubmed) and can help
Comment: Redirection of Duplicate PMIDs
by
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4.2k
how is this query itself originating?
Comment: Redirection of Duplicate PMIDs
by
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• 0
I was able to come up with a workaround using the requests library: import requests pmid = 30134295 url = 'https://pubmed.ncbi…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Thanks for you answer! Actually I have already filtered my peak according to blacklist by bedtools. You mean it's meaningless to compare on…
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141k
More than likely not since the database query seems to work for the redirected PMID but not the original. $ esearch -db pubmed -query …
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Blast showed PDB: 8J07_n9(human) as best template with 62.99%. I also used swissmodel to model the protein and it showed: https://swissmod…
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Pierre Lindenbaum
161k
No, in haplotypecaller
Comment: How to slice a gvcf file with tabix?
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Sd
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Then what is the best way to do slicing for 1Mb windows? Doing `--intervals` in the GenomicsDBImport?
Comment: How to slice a gvcf file with tabix?
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161k
> What is your suggestion to run GenomicsDBImport efficiently? call the GVCF by slices eg: chr1:1000000-2000000<br> run GenomicsDBImport …
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I want to run gatk `GenomicsDBImport` tool to build a GenomicsDB. I want to slice it to reduce the computation time since I have 1300 gvcf …
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The first step has to be taken outside of PLINK here. E.g. append "_1" and "_2" to the duplicated IDs in the .ped or .fam file, then menti…
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Show us the exact call to `cnetplot()` with a sample of all input parameters. Did you compare notes with your friend?
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