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1,000 results • Page
3 of 20
Sort: Votes
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Views
Votes
Replies
10
votes
4
replies
1.4k
views
How to pipe samtools mileup with varscan trio caller?
varscan
samtools
pipe
3.2 years ago by
DareDevil
★ 4.3k
10
votes
1
reply
3.5k
views
RNA-SeQC, EVER-seq, RSeQC and CollectRnaSeqMetrics, which to use and *why*?
RNA-Seq
qc
updated 19 months ago by
Ram
43k • written 8.8 years ago by
Niek De Klein
★ 2.6k
10
votes
14
replies
4.8k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig
read-length
deeptools
ATAC-seq
updated 9 months ago by
Ram
43k • written 4.1 years ago by
gable_works
▴ 50
10
votes
8
replies
1.7k
views
File Format - Fasta
sequence
8.0 years ago by
Gabe Anderson
▴ 10
10
votes
6
replies
2.8k
views
which language to use for such a bioinformatics web services infrastructure?
web-services
java
updated 12 months ago by
Ram
43k • written 8.8 years ago by
lait
▴ 180
10
votes
25
replies
3.4k
views
The interpretation of PCA
DESeq2
R
PCA
updated 5.7 years ago by
Biostar
20 • written 5.7 years ago by
Za
▴ 140
10
votes
11
replies
1.5k
views
How to identify dysregulated pathways using Support Vector machine (SVM)?
SVM
5.3 years ago by
Chaimaa
▴ 260
10
votes
9
replies
2.0k
views
How to improve fastq quality based on fastqc output ?
RNA-Seq
5.9 years ago by
Angelique
▴ 10
10
votes
11
replies
9.0k
views
How to adjust my manhattan plot to look better?
qqman
manhattan
R
updated 22 months ago by
Ram
43k • written 9.0 years ago by
SheelS
▴ 40
10
votes
5
replies
2.4k
views
error with samtools
RNA-Seq
updated 7.1 years ago by
Biostar
20 • written 7.3 years ago by
mra8187
▴ 20
10
votes
5
replies
5.5k
views
Intron Retention And Alternative 5'3' Splice Site Identification
updated 10.2 years ago by
Biostar
20 • written 12.9 years ago by
Arun
2.4k
10
votes
10
replies
3.8k
views
Parameter optimization STAR
RNA-Seq
6.1 years ago by
XBria
▴ 90
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database
analysis
ontology
pathway
updated 9 months ago by
Ram
43k • written 8.0 years ago by
Pranavathiyani G
▴ 330
9
votes
13
replies
3.3k
views
Python Script to map reads to reference sequence
sequence
python
mapping
script
reference sequence
4.9 years ago by
Fid_o
▴ 40
9
votes
5
replies
1.2k
views
how to retrieve all proteins related to cancer
proteins
7.9 years ago by
Learner
▴ 280
9
votes
7
replies
3.3k
views
Aligning Miseq With Deletions >10 Bases
alignment
miseq
next-gen
updated 10.7 years ago by
Biostar
20 • written 11.2 years ago by
Leszek
4.2k
9
votes
13
replies
1.6k
views
SNP's and Gene?
SNP
gene
4.4 years ago by
imgapgenomika
▴ 10
9
votes
11
replies
1.5k
views
6 follow
Split up excel cell into multiple records
excel
byonic
6.7 years ago by
rshipman
▴ 30
9
votes
5
replies
5.2k
views
Binning of reads vs. binning of contigs in metagenomics
Binning
Metagenomics
5.4 years ago by
vijinim
▴ 100
9
votes
10
replies
2.7k
views
About GATK4 Mutect2 runtime (Whole Exome seq)
GATK
Whole Exome Sequencing
Mutect2
3.2 years ago by
kwanghoon
▴ 20
9
votes
5
replies
673
views
Prophage prediction tool
prophage
PHASTER
prediction
updated 8 months ago by
GenoMax
140k • written 8 months ago by
A_heath
▴ 160
9
votes
10
replies
2.2k
views
[solved] Convert fold changes of multiple transcripts of a given gene to a single value characterising this gene
RNA-Seq
7.5 years ago by
biostart
▴ 370
9
votes
16
replies
1.8k
views
feature extraction from SNPs in R
R
gene
sequence
SNP
5.4 years ago by
bioinfo456
▴ 150
9
votes
7
replies
2.6k
views
Averaging duplicates of a gene in RNA-Seq dataset
expression
differential
average
R
rna-seq
updated 2.7 years ago by
biomon
▴ 60 • written 2.7 years ago by
mohammedtoufiq91
▴ 240
9
votes
7
replies
3.7k
views
7 follow
Are 2 replicates per sample sufficient for RNA-seq data analysis?
RNA-Seq
R
Ngs
6.1 years ago by
Arindam Ghosh
▴ 510
9
votes
4
replies
1.3k
views
Is there any method to run tophat ?
RNA-Seq
updated 5.6 years ago by
Biostar
20 • written 5.7 years ago by
Chan
• 0
9
votes
17
replies
2.1k
views
Creating intergenic bam file
R
genome
intergenic
alignment
7.6 years ago by
erincyurtman
• 0
9
votes
12
replies
1.4k
views
Copy number variations analysis
R
CNV
updated 4.3 years ago by
zx8754
11k • written 4.3 years ago by
rprog008
▴ 70
9
votes
13
replies
14k
views
GC Content of Fasta file --- Python Help
sequence
7.1 years ago by
Patrick Brennan
▴ 50
9
votes
19
replies
2.3k
views
There are any way to use a script for feed emboss with fasta sequence?
sequence
4.2 years ago by
schlogl
▴ 160
9
votes
6
replies
3.0k
views
Bug in JellyFish and DSK k-mer counting tool?
dsk
jellyfish
k-mer
7.3 years ago by
scchess
▴ 640
9
votes
6
replies
1.8k
views
Question about featureCounts
RNA-Seq
featurecounts
updated 2.7 years ago by
wang-yanfang
• 0 • written 4.5 years ago by
chichaochen
▴ 30
9
votes
6
replies
3.4k
views
SOAPaligner 2.21 - does it replace all Ns by Gs in reads?
Soapaligner
alignment
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
Philipp Bayer
8.3k
9
votes
2
replies
3.1k
views
GEOquery Problems to Get GEO dataset
Geoquery
8.0 years ago by
Shicheng Guo
★ 9.4k
9
votes
4
replies
5.5k
views
How to analyse normalized read count?
RNA-Seq
R
updated 14 months ago by
Ram
43k • written 8.8 years ago by
pbio
▴ 150
9
votes
10
replies
3.4k
views
generation of heat map by excel data.
R
excel
heatmap
updated 5.8 years ago by
Ram
43k • written 5.8 years ago by
abhilashreddy495
▴ 10
9
votes
4
replies
2.1k
views
[Code] Converte fasta/fa files to fastq
perl
fastq
sed
fasta
updated 19 months ago by
Ram
43k • written 8.4 years ago by
Shicheng Guo
★ 9.4k
9
votes
7
replies
5.5k
views
fisher test with multiple samples
statistics
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
juncheng
▴ 220
9
votes
13
replies
2.3k
views
single tumor vs multiple normal sample differential gene expression (RNA-Seq ) analysis using DESeq2
RNA-Seq
DESeq2
updated 2.9 years ago by
Ram
43k • written 2.9 years ago by
sumitguptabt
▴ 30
9
votes
7
replies
1.1k
views
ChIP-seq; investigate binding within region of tRNA genes
tRNA
ChIP
nf-core
ChIP-seq
updated 22 months ago by
Ram
43k • written 23 months ago by
2138493o
▴ 20
9
votes
8
replies
1.6k
views
Union of unaligned fastq reads
RNA-Seq
6.8 years ago by
Jeffin Rockey
★ 1.3k
9
votes
7
replies
1.9k
views
Is the sequence quality good enough?
WGS
HISEQ4000
QC
5.8 years ago by
BioinfGuru
★ 1.6k
9
votes
7
replies
5.3k
views
How to combine a different sources of pathway database (KEGG, BioCarta) for Pathway analysis.
Pathway
enrichment analysis
GWAS
pathway analysis
7.8 years ago by
kmsh410
▴ 40
9
votes
3
replies
7.1k
views
Statistical Distributions In Rna-Seq Data Analysis
statistics
rna
updated 5.0 years ago by
Biostar
20 • written 12.0 years ago by
Ngsnewbie
▴ 380
9
votes
10
replies
2.4k
views
why there is 0/0 genotyp in VCF file?
VCF
GATK
Variant
4.6 years ago by
star
▴ 350
9
votes
11
replies
4.4k
views
please someone help me with running mirdeep2
software error
mirdeep2
perl
7.5 years ago by
zizigolu
★ 4.3k
9
votes
4
replies
1.6k
views
On which branch in bioinformatics should a cancer researcher focus on ?
cancer
updated 11 months ago by
Ram
43k • written 7.6 years ago by
Bilal
▴ 60
9
votes
20
replies
4.1k
views
Solve SAM issues flagged by Picard's ValidateSamFile
Picard
SAM
updated 12 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
9
votes
11
replies
8.1k
views
8 follow
Extremely low mapping rates with bowtie2
alignment
next-gen
updated 6.4 years ago by
Biostar
20 • written 6.5 years ago by
Sachin
▴ 10
9
votes
16
replies
3.7k
views
6 follow
covert SAM to full length fasta
fasta
SAM
updated 12 months ago by
Ram
43k • written 5.6 years ago by
marongiu.luigi
▴ 710
1,000 results • Page
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Comment: convert cds to seurat object
by
edoardofilippi1998
• 0
Did you check the data in the assay of the cell_data_set object?
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
use the output of `samtools mpileup`
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
ATpoint
81k
It's `-log10(pvalue)`, you miss the minus. Some people use indeed pvalue, but since you're filtering on padj, I would show `-log10(padj)` r…
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
Thank you for your reply!! My bad. I didn't mention that I want to get the mismatch rate for each site. Is this error rate for each site?
Comment: Interproscan taking so much time
by
dthorbur
★ 1.7k
Parallelize. Chunk your transcriptome into groups of something like 5000 (or less if you want it to go faster), and run an array across you…
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Ah, sorry, I was thinking of the wrong command. You can either use `seqtk sample` or `seqkit sample`. I would recommend the former if your …
Comment: Variant calling of GBS data
by
analyst
▴ 10
It does not output warning when I skip flags for MQRankSum and ReadPosRankSum **java -jar -Xmx30G gatk.jar VariantFiltration -R reference…
Comment: Merging featureCounts output for different species
by
andrebolerbarros
• 0
Is there any list of homology you could use for this merging? Maybe this would be helpful
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
again, remove the spaces " "SOR > 10." -> " "SOR>10"
Comment: Variant calling of GBS data
by
analyst
▴ 10
It is still giving same warning java -jar -Xmx30G gatk.jar VariantFiltration -R reference.fa -V A_raw_snps.vcf -O A_filtered_snps.vcf --fi…
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
dzisis1986
▴ 70
It doesn't make sense how to change the threads and in my case it is not working! What kind of problem is that ? is it related to Amazon to…
Comment: STAR aligner options
by
theophile
• 0
I have finally found out the reason behind this behavior. As [pointed out by dsull][1], the beginning of the alignment of read1 to the rat…
Comment: Variant calling of GBS data
by
analyst
▴ 10
Right Pierre, thanks.
Comment: Variant calling of GBS data
by
Pierre Lindenbaum
160k
remove spaces in expressions. 'MQRankSum<0.4'
Comment: Variant calling of GBS data
by
analyst
▴ 10
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