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90,468 results • Page
1 of 1810
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Votes
Replies
0
votes
10
replies
282
views
File conversion from coordinates to genes
conversion
updated 18 minutes ago by
GenoMax
99k • written 16 days ago by
storm1907
• 0
2
votes
1
reply
2.0k
views
Phylobayes, Tracecomp Output Interpretation
updated 44 minutes ago by
Carolina Alejandra
• 0 • written 7.3 years ago by
5heikki
9.7k
0
votes
1
reply
15
views
X amino acid in ensembl
aminoacid
alignment
ensembl
protein
sequence
updated 36 minutes ago by
GenoMax
99k • written 45 minutes ago by
Jason
• 0
0
votes
0
replies
9
views
Forum:
differential expression analysis
DEGS
THRESOLD
CRITERIA
58 minutes ago by
au.rinki.bio
▴ 10
0
votes
0
replies
16
views
List of codon numbers in a panel
browser
codon
list
ucsc
genome
2 hours ago by
ines
• 0
580
votes
155
replies
64k
views
89 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
handbook
tutorial
training
News
updated 5 days ago by
Biostar
10 • written 4.4 years ago by
Istvan Albert
87k
0
votes
0
replies
13
views
SECAPR issue
SECAPR
reads
trimmomatic
pipeline
alignement
2 hours ago by
Begonia_pavonina
▴ 20
0
votes
1
reply
26
views
bulk RNA-seq contamination, lung ambient RNA
mouse
bulkRNAseq
contamination
RNAseq
analysis
updated 1 hour ago by
jared.andrews07
9.2k • written 2 hours ago by
Lpak
• 0
5
votes
10
replies
116
views
6 follow
Multiqc raises the "cannot import name 'gcd' from 'fractions'" error
multiqc
linux
rna-sq
1 hour ago by
sabbirakhand25
• 0
0
votes
1
reply
52
views
Multiply BED scores by a normalization factor in precise intervals in Granges object.
R
3 hours ago by
massimofaggiani
• 0
4
votes
4
replies
69
views
Which Fasta file and GTF file to use in STAR alignment
STAR
ENSEMBL
GTF
fa
3 hours ago by
peru
• 0
0
votes
0
replies
19
views
how to combined peak score or other quantitative indicator when identify TF target gene
ChIP-Seq
4 hours ago by
shangguandong1996
▴ 10
2
votes
2
replies
88
views
How to set variant FILTER in a VCF file based on overlap with regions in a BED file
annotation
bed
vcf
4 hours ago by
William
★ 4.8k
6
votes
5
replies
259
views
Forum:
R - A bioinformatic analysis programming language for NGS
bioinformatics
R
NGS
BI
updated 1 hour ago by
Gjain
5.6k • written 1 day ago by
guoxuantong
▴ 120
2
votes
6
replies
104
views
Meaning letters in TCGA sample barcode field
GDC
Barcode
TCGA
7 hours ago by
sumitguptabt
• 0
1
vote
0
replies
30
views
Methylation frequency + and - strand
methylation
Bismark
8 hours ago by
Palgrave
▴ 30
0
votes
0
replies
28
views
Error : Fail to open file file.vcf for normalization with vt
normalization
vt
vcf
8 hours ago by
Sar
• 0
0
votes
2
replies
80
views
Salmon Script Troubleshooting for RNA Seq Data
NextGenerationSequencing
RNAseq
Bash
Slurm
Salmon
updated 8 hours ago by
ATpoint
48k • written 19 hours ago by
makylakb
• 0
0
votes
0
replies
46
views
Adjusting for the effect of other variables for DGEA in EdgeR
RNASeq
edgeR
DGEA
8 hours ago by
emilien.hourquet
• 0
1
vote
1
reply
56
views
Normalisation before edgeR for RNA-Seq
rna-seq
edgeR
updated 8 hours ago by
ATpoint
48k • written 9 hours ago by
ZheFrench
▴ 320
0
votes
1
reply
44
views
MASURCA output
masurca
updated 3 hours ago by
Carambakaracho
★ 2.4k • written 8 hours ago by
kilcdincer
▴ 10
0
votes
3
replies
68
views
short length amino acids
short
amino
acids
alignment
length
updated 6 hours ago by
GenoMax
99k • written 8 hours ago by
desptsp
• 0
0
votes
1
reply
233
views
comparing enriched GO terms between species
RNA-Seq
go
annotation
updated 8 hours ago by
babalyigit
• 0 • written 9 months ago by
martinaweil
• 0
2
votes
4
replies
208
views
MASURCA error for multiple entries
masurca
updated 7 hours ago by
Kevin Blighe
72k • written 6 days ago by
kilcdincer
▴ 10
0
votes
0
replies
28
views
Including ambiguous samples in DGE as sensitivity analysis
Sensitivity
Limma
DGE
9 hours ago by
mdrnao
• 0
4
votes
11
replies
163
views
Download all Bacteria accession list from NCBI
number
accession
NCBI
3 hours ago by
K.Gee
▴ 40
0
votes
0
replies
48
views
Correlation test based on position sliding window for multiple variables
statistics
R
corr.test
8 hours ago by
User000
▴ 440
0
votes
1
reply
49
views
Precision of variant calling (INDELs)
INDELs
hap.py
updated 6 hours ago by
desouzareis.r
▴ 220 • written 10 hours ago by
esimonova.me
▴ 10
0
votes
0
replies
31
views
DEG list turn into keggscape
Cytoscape
RNA-Sequencing
10 hours ago by
ashwing.kofficial
• 0
0
votes
0
replies
65
views
How can I slicing to RS4 type in rpy2?
rpy2
slicing
rs4
rpy
11 hours ago by
dxodnd
• 0
0
votes
0
replies
66
views
Trycycler Assembly_Issue in Flye and MInimap2
Flye
minimap2
Trycycler
11 hours ago by
Shiv_2
• 0
0
votes
1
reply
84
views
Combining results tables to plot automatecally
DESeq2
updated 11 hours ago by
swbarnes2
9.7k • written 13 hours ago by
hydrobeanz
• 0
1
vote
1
reply
89
views
R command worked yesterday, but stalls today?
R
updated 12 hours ago by
Mensur Dlakic
★ 10k • written 12 hours ago by
cthangav
• 0
0
votes
0
replies
62
views
Cytoscape: Advice on best analysis methods for PPI network
ontology
network
gene
PPI
cytoscape
12 hours ago by
Haley
• 0
0
votes
2
replies
98
views
scRNASeq equal number of cells across conditions
scRNAseq
seurat
updated 1 hour ago by
ATpoint
48k • written 12 hours ago by
TriS
★ 4.3k
0
votes
0
replies
956
views
How to design WGCNA: one analysis over all sample or seperate analysis (using consensus module analysis)?
WGCNA
RNA-seq
14 hours ago by
leesooyeon94
• 0
0
votes
0
replies
49
views
Job:
HIRING: Postdoctoral Scholar in Genomic Epidemiology
epidemiology
genomics
bioinformatics
postdoc
17 hours ago by
genomicshr
▴ 30
0
votes
0
replies
36
views
How to filter and impute missing snps in vcf file
Imputation
SNPs
PLINK
VCF
19 hours ago by
Manoj
▴ 100
2
votes
2
replies
87
views
Arlequin
phylogeny
Bioinformatics
16 hours ago by
Matthew Aaron
• 0
0
votes
1
reply
59
views
How to verify putative miRNA
BLAST
miRNA
putative
Automate
updated 9 hours ago by
jens
• 0 • written 22 hours ago by
arcanjomjr
• 0
0
votes
0
replies
41
views
low unique mapped reads from STAR
sequencing
rnaseq
Alignment
star
updated 21 hours ago by
GenoMax
99k • written 21 hours ago by
dorentinah
• 0
0
votes
0
replies
42
views
samtools depth and sambamba depth produce different results
sambamba
samtools
depth
coverage
21 hours ago by
Johannes
• 0
2
votes
2
replies
325
views
comprehensive bacterial phylogenetic tree with edge lengths for all of RefSeq or Genbank at NCBI?
refseq
ncbi
tree
phylogeny
updated 20 hours ago by
5heikki
9.7k • written 1 day ago by
cmo
▴ 70
1
vote
1
reply
50
views
Checking for(a ton of) overrepresented sequences origins from 16S sequencing
Overrepresented
Amplicon
Blast
FastQC
Illumina
updated 22 hours ago by
GenoMax
99k • written 22 hours ago by
regisantonioli
▴ 20
0
votes
0
replies
37
views
design matrix considering treatment, timepoints and batches
limma
design
microarray
experimental
22 hours ago by
Iván
▴ 40
0
votes
2
replies
157
views
multiqc report, should I care for "Per Base Sequence Content" module if using metagenomic datasets?
fastqc
multiqc
updated 22 hours ago by
Ram
32k • written 23 hours ago by
v.berriosfarias
▴ 10
0
votes
1
reply
66
views
RNA seq experiment design - two in house cell lines, data analysis with CCLE
experimentdesign
RNAseq
batcheffect
updated 23 hours ago by
swbarnes2
9.7k • written 1 day ago by
zoeyn192666
• 0
1
vote
2
replies
86
views
Extract unmapped reads as pairs from (S/B)AM and create corresponding split read files.
bam
sam
unmapped
paired
fastq
10 hours ago by
jens
• 0
6
votes
2
replies
71
views
How to rename/replace the multiline fasta subsequence header in a fasta file?
DNA
alignment
fasta
RNA
1 day ago by
sunnykevin97
▴ 380
3
votes
5
replies
389
views
Intall MAGIC-BLAST in Ubuntu from BASH SHELL in windows powershell.
magicblast
ncbi
ubuntu
linux
powershell
updated 6 months ago by
GenoMax
99k • written 6 months ago by
jjvelazcoa
• 0
90,468 results • Page
1 of 1810
Recent Votes
A: Handling biological replicates across batches in DESeq2
C: Handling biological replicates across batches in DESeq2
Answer: Multiqc
Comment: Multiqc
Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
Answer: Multiqc
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Recent Replies
Comment: How to download via biopython (proteom or genome) individual or random organisms
by
GenoMax
99k
You will need to click through on an entry until you get to page ([example LINK][1]) where you can select all proteins and download them as…
Comment: How to download via biopython (proteom or genome) individual or random organisms
by
ja4123
• 0
Less by PDB. Going back to the example (100 randomly selected bacteria) in the link you put in there is a download option (you can select 1…
Comment: File conversion from coordinates to genes
by
storm1907
• 0
At this moment, this command line helped to me: awk -F'\t' 'BEGIN{OFS=FS} $4 == "" {$4 = "UNKNOWN"} 1' mapped.positions.bed > outfile
Comment: X amino acid in ensembl
by
GenoMax
99k
`ENSMEUP00000002410` identifier s[eems to be pulling up][1] *Tammar wallaby* entries. [1]: http://www.ensembl.org/Multi/Search/Results?…
Comment: Tools for hard trimming?
by
v.berriosfarias
▴ 10
the primers are part of the read? didnt know that, I was concerned about the adapters, but the fastqc report show no info of adapter sequen…
Answer: Phylobayes, Tracecomp Output Interpretation
by
Carolina Alejandra
• 0
Hello! I still have the same question. I am running molecular dating analyses with Phylobayes and some of the parameters have converged b…
Comment: Multiqc raises the "cannot import name 'gcd' from 'fractions'" error
by
sabbirakhand25
• 0
Thanks for the help.
Comment: bulk RNA-seq contamination, lung ambient RNA
by
jared.andrews07
9.2k
What makes you think these are contaminating reads from non-T cells rather than the result of location-specific expression? If your sort lo…
Comment: Trimmomatic-0.36 not finding adapter directory
by
GenoMax
99k
> Ran out of data in the middle of a fastq entry. Your file is probably > truncated at That is not good news. It appears that your trimmed…
Comment: Trimmomatic-0.36 not finding adapter directory
by
Istvan Albert
87k
how big is your data? how many reads do you have. trimmomatic is fairly efficient and fast - but in the end it all depends on the amount of…
Comment: Trimmomatic-0.36 not finding adapter directory
by
willbrown
• 0
Hi, thank you for the reply. I tried your path idea and it worked, with no error messages following. However, my terminal was unresponsive …
Comment: File conversion from coordinates to genes
by
storm1907
• 0
Yes, I try to convert empty space to string, but without success: awk 'BEGIN {OFS=FS="\t"} {gsub(/" "/,"na",$4)}1' $file > $outfile1
Comment: File conversion from coordinates to genes
by
GenoMax
99k
Because you have gene names missing from some of your rows you are getting that error.
Comment: scRNASeq equal number of cells across conditions
by
TriS
★ 4.3k
thank you, yes, I added some extra info above to help. the main point is that working with immunologists they always want to know the abund…
Comment: How to perform multiple alignment using MAFFT?
by
anikcropscience
▴ 40
Hi @ram Sorry for the delay. My vpn contract ended and had to renew it. So, I see the problem. After running the code `system(paste0("cat…
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