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117 results • Page
1 of 3
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Votes
Replies
25
votes
13
replies
25k
views
8 follow
Bowtie2 parameters for best alignment
alignment
Assembly
genome
SNP
updated 6 hours ago by
Medhat
9.5k • written 8.8 years ago by
cvu
▴ 180
12
votes
4
replies
15k
views
Command to extract SNPs from VCF file using bcftool
SNPs
bcftools
VCF
updated 6 hours ago by
Ram
38k • written 6.9 years ago by
MAPK
★ 2.0k
12
votes
7
replies
3.0k
views
Forum:
Which is better for job opportunities: Metagenomics OR Plant biotechnology
Metagenomics
Plant-biotechnology
career
updated 5 hours ago by
Ram
38k • written 7.9 years ago by
anokimchen
• 0
9
votes
4
replies
308
views
Snakemake, snake files
Snakemake
updated 6 hours ago by
Ram
38k • written 4 months ago by
beginner123
• 0
9
votes
6
replies
390
views
6 follow
split fasta file to train deep learning model
fasta
split
bash
R
updated 16 hours ago by
shenwei356
7.9k • written 1 day ago by
pinheirofabiano
▴ 10
8
votes
9
replies
5.1k
views
gene filtering for agilent microarray using Limma
agilent microarray
limma
gene filtering
R
updated 6 hours ago by
Kevin Blighe
84k • written 7.6 years ago by
rohit
▴ 60
7
votes
20
replies
1.9k
views
NcbiblastpCommandline alignment results are different from blast webpage
alignment
biopython
blastp
updated 6 hours ago by
Ram
38k • written 11 months ago by
laila.jafari
• 0
7
votes
6
replies
455
views
Nextflow: No space left on device, process using output directory as input?
nextflow
updated 15 hours ago by
Maxime Garcia
▴ 230 • written 3 days ago by
Eliveri
▴ 320
6
votes
9
replies
4.7k
views
Best Possible set of Python interview questions for Bioinformatics, that a recruiter can ask?
python
updated 4 hours ago by
Ram
38k • written 7.9 years ago by
gaurav.singh
▴ 10
6
votes
5
replies
342
views
Where do find virulence gene information in a gff/gtf file?
microbial
genomics
gff
annotation
gtf
updated 10 hours ago by
oschwengers
▴ 100 • written 1 day ago by
sovrappensiero
▴ 60
5
votes
3
replies
356
views
News:
March 13-16: Virtual Nextflow and nf-core training event in 5 languages
nf-core
pipeline
Nextflow
updated 16 hours ago by
Maxime Garcia
▴ 230 • written 4 weeks ago by
Matthias Zepper
3.4k
5
votes
9
replies
550
views
Calculate RPKM
RPKM
3 hours ago by
Chris
▴ 70
5
votes
11
replies
5.8k
views
[HuEx-1_0-st] Affymetrix Human Exon 1.0 ST Array [transcript (gene) version]
HuEx-1_0-st
R
updated 6 hours ago by
Ram
38k • written 5.0 years ago by
vinnu260
▴ 20
4
votes
8
replies
2.3k
views
7 follow
Converting an output de-novo transcriptome assembled with Trinity to a .gff3 file
Trinity
updated 12 hours ago by
Juke34
7.7k • written 3.5 years ago by
Raito92
▴ 80
4
votes
3
replies
1.1k
views
Want to create a new Index file for BAM using SAMTOOLS. Do I need to sort the default BAM file from Dante Labs First?
WGSExtract
Dante-Labs
samtools
updated 6 hours ago by
Ram
38k • written 2.7 years ago by
Umesh
• 0
4
votes
5
replies
1.6k
views
How to apply for bioinformatics jobs
career
updated 5 hours ago by
Ram
38k • written 8.0 years ago by
nitikagupta526
• 0
4
votes
4
replies
247
views
Trying to install Roary with Conda results in error message
roary
conda
updated 4 hours ago by
Ram
38k • written 15 hours ago by
tobiwan
▴ 10
4
votes
2
replies
7.9k
views
What is the best practice for BAM sorting?
RNA-Seq
samtools
STAR
updated 4 hours ago by
Ram
38k • written 7.9 years ago by
Kirill Tsyganov
▴ 350
4
votes
3
replies
1.8k
views
Forum:
possible bug: can make minia run forever with a bogus FASTA
minia
updated 5 hours ago by
Ram
38k • written 8.0 years ago by
adam.ewing
• 0
4
votes
7
replies
507
views
How to perform synteny alignments and plots only with a gene?
Comparative
Evolution
Alignment
Synteny
Genomics
updated 3 hours ago by
cmdcolin
★ 2.9k • written 3 days ago by
Rafael Soler
★ 1.1k
3
votes
3
replies
400
views
extracting contigs
fasta
grep
updated 6 hours ago by
Ram
38k • written 5 months ago by
hollyannj7
• 0
3
votes
5
replies
211
views
samtools idxstats not removing ChrM
samtools
ChIPseq
updated 4 hours ago by
benformatics
3.5k • written 14 hours ago by
Jen
▴ 40
3
votes
2
replies
1.5k
views
Forum:
Invitation Research Collaborations
cancer
R
next-gen-sequencing
updated 5 hours ago by
Ram
38k • written 7.9 years ago by
alexandru.floares
▴ 30
3
votes
6
replies
514
views
Chromosome "whole genome shotgun sequence" not found
samtools
mpileup
7 hours ago by
Hayler Edu
▴ 30
3
votes
2
replies
286
views
Human Population Reference Genomes (+Neanderthal?)
comparative-genomics
updated 7 hours ago by
Ram
38k • written 2 days ago by
emm008
• 0
3
votes
2
replies
1.3k
views
Criteria for merging multiple VCF files
bcftools
VCF
updated 6 hours ago by
Ram
38k • written 3.3 years ago by
seta
★ 1.7k
3
votes
0
replies
2.6k
views
Job:
Software engineer position in computational biology and high-performance/cloud computing (New York City)
HPC
Genomics
Software
Machine-learning
updated 4 hours ago by
Ram
38k • written 7.9 years ago by
pandey.gaurav
▴ 190
3
votes
2
replies
317
views
Tools to calculate coverage of a bam file window by window
gatk
coverage
samtools
bam
deeptools
updated 6 hours ago by
Ram
38k • written 3 months ago by
marion.prieler
▴ 10
3
votes
9
replies
5.8k
views
bcftools doesn't normalize the vcf file
vcf
bcftools
normalize
updated 6 hours ago by
Ram
38k • written 4.2 years ago by
seta
★ 1.7k
3
votes
3
replies
366
views
Downloading required resources for VQSR
VQSR
WGS
sequencing
genome
WES
updated 6 hours ago by
Ram
38k • written 5 weeks ago by
Yoosef
▴ 50
3
votes
3
replies
334
views
Subseq bam file
bam
subseq
updated 6 hours ago by
Ram
38k • written 3 months ago by
Jjbox
▴ 40
3
votes
4
replies
469
views
Changing Temporary File Location for Local BLASTP to nr Database
protein
blast
nr
updated 6 hours ago by
Ram
38k • written 9 weeks ago by
katieostrouchov
▴ 20
3
votes
4
replies
2.5k
views
Error in systemPipeR
r
systemPipeR
updated 6 hours ago by
Ram
38k • written 8.1 years ago by
Parham
★ 1.6k
2
votes
2
replies
217
views
FastQ file not recognized by hisat2 allignment
hisat2
rnaseq
rna-seq
nextflow
updated 17 hours ago by
Maxime Garcia
▴ 230 • written 1 day ago by
selenaajohn
• 0
2
votes
0
replies
2.2k
views
Job:
Scientific Programmer - Vertebrate Genomes, EMBL-EBI, Cambridge UK, closes 17th April
ChIP-Seq
alignment
RNA-Seq
SNP
updated 5 hours ago by
Ram
38k • written 7.9 years ago by
Laura
★ 1.8k
2
votes
2
replies
1.7k
views
Forum:
Features for an electronic lab notebook
notebook
updated 4 hours ago by
Ram
38k • written 7.9 years ago by
jeff.mcwhirter
▴ 20
2
votes
2
replies
357
views
STAR can't genereate genome Index.
STAR
updated 6 hours ago by
Ram
38k • written 4 months ago by
e183021g
▴ 10
2
votes
2
replies
351
views
How do I create input files required by iGEAK (or find alternatives to iGEAK) for array analysis.
iGEAK
mirna
updated 6 hours ago by
Ram
38k • written 4 months ago by
Bhanu
• 0
2
votes
8
replies
2.0k
views
Sift on the VEP output
missense-variant
SIFT
SNP
VEP
updated 6 hours ago by
Ram
38k • written 4.4 years ago by
mostafarafiepour
▴ 160
2
votes
4
replies
2.0k
views
BioPython: Residues size differ from position
Biopython
Protein-database
updated 6 hours ago by
Ram
38k • written 8.0 years ago by
rod.god
• 0
2
votes
2
replies
247
views
Nextflow Stringtie: command not found Error
nextflow
rna-seq
stringtie
updated 13 hours ago by
ATpoint
70k • written 2 days ago by
selenaajohn
• 0
2
votes
2
replies
285
views
Divide reads to shorter reads in Fastq file
Fastq
updated 6 hours ago by
Ram
38k • written 3 months ago by
Ahiad Chen Zion
• 0
2
votes
5
replies
541
views
Per sample information from a multi sample vcf file
vcf
updated 6 hours ago by
Ram
38k • written 3 months ago by
Peerzada
• 0
2
votes
3
replies
883
views
What is the difference between Average Nucleotide Identity (ANI) and blastn analysis?
alignment
blast
sequence
updated 4 hours ago by
Ram
38k • written 2.2 years ago by
Kumar
▴ 90
1
vote
2
replies
77
views
How to adjust for multiple batches using Combat-Seq
ComBat
RNA-seq
updated 4 hours ago by
Ram
38k • written 4 hours ago by
sabriledesma13
• 0
1
vote
3
replies
132
views
How to extract/find the actual names of the gene_IDs if they are not fully presented in gtf.file, and link them to the Count.matrix
featureCounts
gtf
RNA-Seq
updated 4 hours ago by
GenoMax
126k • written 7 hours ago by
Pegasus
▴ 80
1
vote
2
replies
115
views
how to get pfam id of proteins belonging to a particular family along with sequences in that family?
pfam
protein
id
interpro
sequence
updated 12 hours ago by
GenoMax
126k • written 12 hours ago by
max
• 0
1
vote
0
replies
1.7k
views
Job:
COMPUTATIONAL BIOLOGIST, Ph.D
statistics
next-gen
software
code
updated 5 hours ago by
Ram
38k • written 8.0 years ago by
danielle
▴ 30
1
vote
1
reply
1.4k
views
Error: Sieve v.2.2 (Label-free mass spectrometery differential analysis) - Index bounds outside the array
LFQ
Mass-Spectrometry
LC-MS-MS
updated 6 hours ago by
Ram
38k • written 4.6 years ago by
Ramaraj K
• 0
1
vote
1
reply
212
views
What is the difference between agilent_wholegenome and agilent_wholegenome_4x44k_v1 in biomart?
genetics
biomaRt
gene
updated 4 hours ago by
Ram
38k • written 1 day ago by
solarchan7
• 0
117 results • Page
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Recent Votes
Comment: Calculate RPKM
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Comment: Trying to install Roary with Conda results in error message
Comment: Trying to install Roary with Conda results in error message
Answer: samtools idxstats not removing ChrM
Comment: samtools idxstats not removing ChrM
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Comment: How can I determine the number of detected genes and detected transcripts/isofor
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That's what I was expecting but I got the opposite where there were more detected genes relative to the number of detected transcripts. Ki…
Comment: How can I determine the number of detected genes and detected transcripts/isofor
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126k
You have this tagged as single cell so assuming that is what the data is referring to perhaps you should have been using `STARsolo` or `ale…
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if you want a 'genome browser' type approach, could try jbrowse 2, I am a developer of it. it has pairwise synteny visualization features l…
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Thank you so much! I figured it out a few hours ago. Could I ask you questions about ATAC-seq?
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the easiest way is to probably take the numeric columns of your data frame and create a matrix. For instance, if column 1 is gene names, an…
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You've [cross-posted this on bioinformatics SE][1]. Don't do that - a bunch of people are on both forums are it is bad etiquette to waste v…
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Even if the batches were meaningfully distributed, OP doesn't need to use ComBat-seq for batch especially when they're trying to do DE - th…
Comment: Processing fastqs generated by inDrop protocol
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i'm just guessing but there is an 8 bp read and a 16 bp read so my guess is those are the non-transcriptomic part (maybe a UMI + cell barco…
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Cancer is nested with batch, meaning batch 4 and cancer is the same thing. There is nothing you can correct for. This analysis is not meani…
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I probably should have used salmon in the first place but wanted to knock-out-2-bird-with-one-stone in creating a wrapper for STAR for anot…
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If you are not sure which file you need, are you sure you're equipped to analyse the data it spits out, or that you are even doing the corr…
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by
GenoMax
126k
Looks like you have already used `featureCounts` which is what would be recommended here. If you want to do transcript level estimations …
Comment: How to extract/find the actual names of the gene_IDs if they are not fully prese
by
GenoMax
126k
You could Convert your annotation file into Simple Annotation Format (SAF) that featureCounts understands. You will need to pull out `GENE_…
Comment: Trying to install Roary with Conda results in error message
by
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The issue is that a package installed via `conda` has dependencies (i.e., other packages it depends upon), and these need not all be mainta…
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by
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38k
Try every file. Or read bismark documentation until you're sure which one you need. I'd recommend the latter approach because it takes less…
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