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101,968 results • Page
1 of 2040
Sort: Rank
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Votes
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0
votes
0
replies
6
views
qPCR Assay plot
barplot
qpcr
R
33 minutes ago by
Maria17
• 0
0
votes
1
reply
35
views
Adding a new protein to similarity matrix based on sequence alignment
protein
similarity
sequence
R
msa
updated 1 hour ago by
Mensur Dlakic
★ 19k • written 2 hours ago by
27b99607
• 0
0
votes
2
replies
18
views
Using fastq-mcf tool
Genomics
updated 1 hour ago by
Ram
36k • written 1 hour ago by
aranyak111
• 0
0
votes
1
reply
119
views
Find markers from multiple groups using bulk RNA-seq data
RNA-seq
findMarkers
bulk
DEG
updated 1 hour ago by
Chris S.
▴ 320 • written 8 weeks ago by
ccfpwll
• 0
0
votes
2
replies
24
views
Error in GATK haplotypecaller running
GATK
updated 1 hour ago by
Ram
36k • written 1 hour ago by
Azhar Jameel
• 0
0
votes
1
reply
1.0k
views
AutoDock needs the extension of the docking parameter file to be ".dpf"?
autodock
docking
autogrid
updated 2 hours ago by
Dr. Osuolale
• 0 • written 2.9 years ago by
arunsaikirans
• 0
2
votes
7
replies
65
views
error while using cyvcf2 to parse the vcf file
error
vcf
cyvcf2
htslib
parsing
30 minutes ago by
rheab1230
▴ 50
0
votes
0
replies
23
views
CNV and DUP in vcf files Gnomad database
dup
cnv
gnomad
vcf
3 hours ago by
arya.sagittarius
• 0
670
votes
160
replies
84k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 5 weeks ago by
Biostar
740 • written 5.5 years ago by
Istvan Albert
93k
6
votes
5
replies
125
views
Forum:
How to learn bioinformatics?
bioinformatics
updated 2 hours ago by
Marco Pannone
▴ 240 • written 4 hours ago by
sakichwan
▴ 10
0
votes
1
reply
46
views
counting snps from alternative allele using tsv format
python
updated 3 hours ago by
Pierre Lindenbaum
145k • written 3 hours ago by
Abdellrhmanakl
• 0
2
votes
2
replies
52
views
What do they mean by "multidomain" and "multimetric"?
protein
protein-structure
protein-structure-prediction
3 hours ago by
user366312
▴ 10
0
votes
2
replies
46
views
R, group data based on names and sum each group
manipulation
R
data
updated just now by
cpad0112
20k • written 3 hours ago by
mthm
▴ 40
0
votes
5
replies
72
views
blast with multithreads is much slower
blast
1 hour ago by
biobiu
▴ 130
0
votes
0
replies
56
views
What conclusions can I draw from a Procrustes Superimposition Test?
Multivariate
Statistics
Procrustes
Correlation
just now by
dch014
• 0
0
votes
3
replies
69
views
GSEA not returning significant gene sets
GSEA
updated 22 minutes ago by
cpad0112
20k • written 4 hours ago by
jabbari.parnian
▴ 20
0
votes
1
reply
44
views
bcl2fastq error: Barcode lengths in the sample sheet do not match those in --use-bases-mask
cellranger
bcl2fastq
CITE
mkfastq
CITE-seq
updated 2 hours ago by
GenoMax
115k • written 4 hours ago by
coteparker
• 0
0
votes
6
replies
117
views
How to create kallisto index that does not include ribosomal genes
rna-seq
enseml
bioinformatics
kallisto
updated 3 hours ago by
Carambakaracho
★ 3.0k • written 5 hours ago by
bioinfo
▴ 10
0
votes
3
replies
75
views
SRR sample ID
TCGAbiolinks
RNA-seq
sampleID
R
cancer
programming
updated 2 hours ago by
Hamid Ghaedi
★ 2.5k • written 4 hours ago by
mahsa
• 0
2
votes
2
replies
144
views
Donwloading latest version of Mouse ref genome
musculus.
Reference
Ensembl
Mus
genome
updated 5 hours ago by
vkkodali_ncbi
★ 3.1k • written 14 hours ago by
salman_96
▴ 50
0
votes
0
replies
30
views
guppy_barcoder - demultiplex- custom barcodes
nanopore
guppy
demultiplex
updated 6 hours ago by
Ram
36k • written 6 hours ago by
henry-keen
▴ 20
0
votes
0
replies
41
views
DESeq2 and WGCNA
DESeq2
RNAseq
WGCNA
6 hours ago by
pthom010
▴ 20
2
votes
5
replies
350
views
How to access the ACLAME server?
ACLAME
6 hours ago by
cloredana20
▴ 10
0
votes
0
replies
33
views
Inferring GRN without transcription factor motif
scenic
GRN
cell
single
6 hours ago by
William
• 0
1
vote
1
reply
62
views
bcl2fastq with unique dual indexing
demultiplexing
UDI
DNAseq
sequencing
updated 6 hours ago by
GenoMax
115k • written 8 hours ago by
ginlucks
▴ 10
0
votes
1
reply
54
views
Msigdb GO:BP
msigdb
updated 6 hours ago by
igor
12k • written 7 hours ago by
AriBo
• 0
0
votes
3
replies
130
views
How to search and identify the function of DEGs
function
functional
annoatation
DEGs
updated 4 hours ago by
Marco Pannone
▴ 240 • written 16 hours ago by
Roy.anupama11
• 0
1
vote
3
replies
130
views
Can I compare different RNAseq experiment DEG lists to see which experiments are the most similar?
DEG
lists
Comparision
RNAseq
updated 6 hours ago by
rpolicastro
8.2k • written 8 hours ago by
rachel.walters.18
• 0
1
vote
0
replies
66
views
Herald:
The Biostar Herald for Monday, May 23, 2022
herald
updated 6 hours ago by
Rob
5.2k • written 8 hours ago by
Biostar
740
0
votes
5
replies
132
views
Method to fill N gaps with de novo assembly
assembly
updated 9 hours ago by
samuel.a.odonnell
▴ 330 • written 10 hours ago by
pablo
▴ 210
0
votes
1
reply
67
views
How can I convert this format of S. tuberosum gene sequence ID - Soltu.DM.10G013850.1 - to Entrez ID?
potatoID
updated 9 hours ago by
Pierre Lindenbaum
145k • written 10 hours ago by
Sanja
• 0
4
votes
13
replies
379
views
Automatic rename of filenames with bash script
rename
bash
script
updated 7 hours ago by
cpad0112
20k • written 2 days ago by
Morta
• 0
0
votes
2
replies
506
views
AGP file ENA submission error
ENA
updated 9 hours ago by
Juke34
★ 6.9k • written 24 months ago by
rob234king
▴ 610
2
votes
3
replies
103
views
Alignments on IGV display not matched to the result from "samtools mpileup"
IGV
Alignments
mpileup
12 hours ago by
magicRG
▴ 20
0
votes
1
reply
75
views
panX no working
panX
error
updated 11 hours ago by
GenoMax
115k • written 13 hours ago by
saifulislam99121
• 0
0
votes
1
reply
81
views
SNP and Phenotype Correlation
Phenotype
Statistical
SNP
Correlation
R
updated 12 hours ago by
dthorbur
▴ 220 • written 13 hours ago by
chimerajit
• 0
0
votes
2
replies
108
views
Ugene for Centos7
centos7
conflicts
ugene
software
updated 3 hours ago by
brian.fristensky
▴ 270 • written 17 hours ago by
Валентин
• 0
0
votes
0
replies
42
views
tr2aacds error about class2pub
tr2aacds
class2pub
error
15 hours ago by
380630938
• 0
0
votes
0
replies
56
views
analyze_diff_expr.pl result explanation
Trinity
analyze_diff_expr.pl
UP.subset
DEGs
15 hours ago by
Roy.anupama11
• 0
0
votes
3
replies
140
views
How to find unique and common genus by comparing 4 different files containing genus ?
genus
level
diversity
unique
common
updated 9 hours ago by
Joe
20k • written 17 hours ago by
Akash Chandra Parida
▴ 40
0
votes
1
reply
168
views
how to create a dataset from fastq sequence files in ubuntu
metagenomics
microbiome
dataset
usearch
ubuntu
updated 20 hours ago by
Mark
★ 1.1k • written 3 days ago by
Flo
• 0
1
vote
9
replies
1.3k
views
Fasterq-dump unexpected parameter error (unexpected parameter[256]: '/home/GEOdata/sra/SRR6687807.sra)
RNA-Seq
software error
updated 12 hours ago by
ATpoint
61k • written 19 months ago by
cwliu0222
• 0
2
votes
2
replies
136
views
pfam functional redundancy
redundancy
protein
pfam
domain
function
20 hours ago by
timothy.kirkwood
▴ 90
5
votes
5
replies
333
views
Should I wait for finishing the BWA MEM alignment?
Bwa
mem.
updated 20 hours ago by
seidel
9.4k • written 1 day ago by
oğuzhan
• 0
0
votes
0
replies
85
views
CNEFinder merge chromosomes
chromosome
concatanate
CNEFinder
1 day ago by
kagan.ferenc
• 0
4
votes
1
reply
221
views
What does it mean by "topology" in the case of secondary and tertiary structures of proteins?
protein
protein-structure
protein-structure-prediction
updated 1 day ago by
Mensur Dlakic
★ 19k • written 1 day ago by
user366312
▴ 10
2
votes
1
reply
130
views
Generating structural embeddings from FaceBook ESM model
alphafold
updated 1 day ago by
Mensur Dlakic
★ 19k • written 1 day ago by
tom5
• 0
1
vote
1
reply
102
views
Demuxlet using Illumina GSA?
global
array
demuxlet
screening
gsa
updated 1 day ago by
cpad0112
20k • written 1 day ago by
kgoss
▴ 10
0
votes
0
replies
73
views
homer not configured properly
Homer
makeTagDirectory
1 day ago by
amahdi779
• 0
2
votes
2
replies
271
views
NGS data analysis
tNGS
6 hours ago by
bookorg
▴ 10
101,968 results • Page
1 of 2040
Recent Votes
A: Ti Tv ratio and their usefulness in exome sequencing
Comment: error while using cyvcf2 to parse the vcf file
Comment: error while using cyvcf2 to parse the vcf file
Comment: Can I compare different RNAseq experiment DEG lists to see which experiments are
Comment: How to learn bioinformatics?
Answer: How to learn bioinformatics?
How to learn bioinformatics?
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Recent Replies
Comment: R, group data based on names and sum each group
by
cpad0112
20k
with R library(dplyr) df %>% group_by(col4,col5) %>% mutate(sum=sum(col6)) %>% ungroup() > with (df, agg…
Comment: GSEA not returning significant gene sets
by
cpad0112
20k
how does the PCA of the normalized counts look? can you see the grouping of samples as per metadata/variables?
Comment: error while using cyvcf2 to parse the vcf file
by
rheab1230
▴ 50
I checked with the above command and it seems like my vcf file is broken: bcftools view chr22_id1.vcf > /dev/null && echo "OK" …
Answer: Adding a new protein to similarity matrix based on sequence alignment
by
Mensur Dlakic
★ 19k
In short: you can't go wrong by re-aligning, and it is possible to go wrong by concocting some kind of similarity matrix without re-alignin…
Comment: Using fastq-mcf tool
by
Ram
36k
I'm sure this has been mentioned to you before (and your post before editing shows you know how to do it), please format code as code where…
Answer: Using fastq-mcf toolk
by
Pierre Lindenbaum
145k
your trying to run the **manual** file ( https://linux.die.net/man/1/intro ) of your tool (`fastq-mcf.1`), not the executable itself there…
Comment: error while using cyvcf2 to parse the vcf file
by
Pierre Lindenbaum
145k
if the command bcftools view chr22_id1.vcf > /dev/null && echo "OK" prints OK and shows no error, then it's a problem with cyvcf2 ot…
Comment: Long variant splits to several variants by variant callers
by
vdauwera
★ 1.2k
To troubleshoot that sort of thing, you need to re-run HaplotypeCaller with the -bamout argument so you can see what it was "thinking". If …
Comment: error while using cyvcf2 to parse the vcf file
by
Pierre Lindenbaum
145k
thanks it *does* look like a vcf.
Comment: blast with multithreads is much slower
by
biobiu
▴ 130
Of course. Things went slow with one thread so I hoped to speed things up a little bit with multithreading. The surprise was not from not …
Comment: Error in GATAK haplotypecaller running
by
Ram
36k
I've changed that tag to GATK. It probably was a language barrier thing.
Comment: error while using cyvcf2 to parse the vcf file
by
rheab1230
▴ 50
The only difference is the ID column; I had to edit the ID column with this format `chr22_16062270_G_T_b37` to do further analysis.
Comment: error while using cyvcf2 to parse the vcf file
by
rheab1230
▴ 50
for command3: grep "#CHROM" -C2 chr22_id1.vcf ##bcftools_annotateVersion=1.13+htslib-1.13 ##bcftools_annotateCommand=annotate -c …
Comment: error while using cyvcf2 to parse the vcf file
by
rheab1230
▴ 50
I have added the output for the above command: for command (1): file chr22_id1.vcf chr22_id1.vcf: ASCII text, with very long lines …
Comment: Error in GATAK haplotypecaller running
by
Pierre Lindenbaum
145k
what is this tag "hannah" ? did you read https://gatk.broadinstitute.org/hc/en-us/articles/360035531652-FASTA-Reference-genome-format >…
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