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116,497 results • Page
1 of 2330
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Votes
Replies
0
votes
2
replies
33
views
bam merging for archaic samples
samtools
bam
ancient
merge
50 minutes ago by
Matteo Ungaro
▴ 100
0
votes
1
reply
43
views
Filtering sam or bam file with maximum matching region
crisper-edited
alignment
match
updated 2 hours ago by
Pierre Lindenbaum
161k • written 4 hours ago by
analyst
▴ 20
0
votes
1
reply
123
views
Removing Illumina microarray probes with no expression HumanHT-12v4
microarray
HumanHT-12v4
Illumina
updated 4 hours ago by
Gordon Smyth
★ 7.0k • written 15 hours ago by
Bioinformatician
• 0
1
vote
0
replies
133
views
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Primers
TRINITY
6 hours ago by
mathavanbioinfo
▴ 90
0
votes
1
reply
163
views
GTF file from Stringtie to R Studio for either Ballgown or DESeq2
Stringtie
Cufflinks
Ballgown
DESeq2
updated 9 hours ago by
Ram
43k • written 13 hours ago by
Nina
• 0
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 weeks ago by
Biostar
2.6k • written 7.4 years ago by
Istvan Albert
100k
1
vote
1
reply
157
views
MEGA Analysis Issue on High-Performance Computer
phylogenetic-analysis
MEGA
updated 11 hours ago by
Ram
43k • written 14 hours ago by
Giorgio
• 0
0
votes
1
reply
175
views
Running blastp with BLAST+ 2.15.0 against custom database; need to identify hits
shotgun
metagenomics
blastp
taxonomy
updated 15 hours ago by
GenoMax
141k • written 17 hours ago by
rebecca.calvo
• 0
0
votes
0
replies
114
views
Using samtools with GCS (google cloud storage) on docker a docker container seems to give "Protocol Not Supported" error
samtools
gcs
16 hours ago by
abhishekghadge
• 0
0
votes
3
replies
312
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 11 hours ago by
Ram
43k • written 17 hours ago by
rheab1230
▴ 140
1
vote
4
replies
404
views
what's the genomic location and name of gene responsible for orange and black patches in calico cats
genomes
updated 16 hours ago by
Matthias Zepper
4.5k • written 19 hours ago by
Ann
★ 2.4k
0
votes
0
replies
101
views
agilent microarray gpl data does not have gene symbol column
microarray
agilent
gpl
updated 18 hours ago by
Ram
43k • written 20 hours ago by
mja
• 0
0
votes
0
replies
104
views
scRNA Cluster frequency
CV
PCA
scRNA
Cluster-Frequency
20 hours ago by
Nitin
• 0
1
vote
5
replies
421
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 17 hours ago by
GenoMax
141k • written 20 hours ago by
Luka
• 0
0
votes
0
replies
110
views
absolute path for symbolic links in Snakefile
Snakemake
updated 20 hours ago by
Ram
43k • written 20 hours ago by
yifangt86
▴ 60
0
votes
0
replies
100
views
Chemical structure validation
structure
cap
validation
metabolite
20 hours ago by
Rodolfo Adrián
• 0
3
votes
8
replies
1.1k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 6 hours ago by
swbarnes2
14k • written 8 months ago by
bp22
▴ 80
0
votes
1
reply
172
views
Downloading the raw microarray data from GEO
.gpr
microarray
.CEL
updated 20 hours ago by
GenoMax
141k • written 21 hours ago by
bioyas
▴ 10
0
votes
0
replies
119
views
Copy number variation plot
Copy-number-variation
genomics
updated 22 hours ago by
Ram
43k • written 22 hours ago by
Emmi
• 0
1
vote
5
replies
584
views
RNA seq differential expression analysis
RNA-seq
normalization
updated 22 hours ago by
BioinfGuru
★ 1.7k • written 2 days ago by
rrehimi
• 0
0
votes
0
replies
103
views
SNP calling with ANGSD and ngsLD. How many SNPs?
lcwgs
ngsTools
ANGSD
genomics
22 hours ago by
DanielEB_fisk
▴ 20
0
votes
1
reply
199
views
Could you please assist in identifying this cluster?
single-cell
updated 22 hours ago by
Ram
43k • written 23 hours ago by
Kazo
• 0
4
votes
9
replies
2.6k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by
dvelmeshev
• 0
2
votes
7
replies
5.2k
views
6 follow
Memory usage of picard Samsort
Picard
SortSam
updated 23 hours ago by
ATpoint
81k • written 7.1 years ago by
boymin2020
▴ 80
5
votes
13
replies
820
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 30 minutes ago by
ATpoint
81k • written 1 day ago by
BioinfGuru
★ 1.7k
1
vote
1
reply
336
views
Plink merge errors.
cygwin64
bed
PLINK
1 day ago by
Dinmukhamed
• 0
0
votes
0
replies
123
views
Conversion to tree format
PLINK
bed
Figtree
SplitsTree
updated 22 hours ago by
Ram
43k • written 1 day ago by
Dinmukhamed
• 0
0
votes
0
replies
124
views
miRDeep2: How to get the read counts
mirdeep2
1 day ago by
Atul K.
• 0
1
vote
2
replies
399
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
rahu
• 0
0
votes
0
replies
131
views
Lncipedia GTF file error
Proteomics
updated 22 hours ago by
Ram
43k • written 1 day ago by
atharvakarkare14
▴ 10
7
votes
3
replies
2.7k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 1 day ago by
colindaven
6.4k • written 15 months ago by
Dr.Animo
▴ 130
3
votes
3
replies
353
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 hours ago by
swbarnes2
14k • written 1 day ago by
joe
▴ 510
0
votes
2
replies
437
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
1 day ago by
航太郎
• 0
0
votes
3
replies
381
views
Adding CB tag to bam file
samtools
bam
updated 6 hours ago by
swbarnes2
14k • written 1 day ago by
Maria
• 0
11
votes
12
replies
818
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 1 day ago by
Ram
43k • written 1 day ago by
iamsmor
• 0
0
votes
0
replies
143
views
create genewise sync file in popoolation
popoolation
updated 1 day ago by
GenoMax
141k • written 1 day ago by
N.Y.Wiyana-Hewage
• 0
0
votes
2
replies
302
views
python file for coding potential calculator
cpc2.py
1 day ago by
Ashok
• 0
0
votes
2
replies
294
views
error in coding potential calculator CPC2
cpc
CPC2
coding-potential
1 day ago by
Ashok
• 0
0
votes
2
replies
329
views
miRNAs quantification using mirdeep2 tool
differential-expression
mirdeep2
miRNA
1 day ago by
Ashok
• 0
5
votes
2
replies
393
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 1 day ago by
shelkmike
★ 1.2k • written 2 days ago by
kirillkirilenko
▴ 40
0
votes
0
replies
148
views
Variant Generation Using Longshot
long-reads
variant-calling
ONT
minion
longshot
updated 1 day ago by
Ram
43k • written 1 day ago by
samuelkalandarov2002
• 0
1
vote
1
reply
304
views
Problem with Mirdeep2 and Randfold output
mirdeep2
Randfold
1 day ago by
otieno43
▴ 30
0
votes
2
replies
349
views
QC exclusion of A/T or G/C alleles to avoid strand issues
quality-control
SNV
QC
SNP
22 hours ago by
_quantum_girl_
▴ 10
0
votes
0
replies
154
views
traying to make a maf from an already annotated vcf
vcf2maf
VEP
maftools
updated 1 day ago by
Ram
43k • written 1 day ago by
Javier
• 0
1
vote
4
replies
632
views
What happened to Tombo Re-squiggle
Tombo
resquiggle
ONT
updated 1 day ago by
Ram
43k • written 3 months ago by
turcoa1
• 0
0
votes
0
replies
149
views
Pruning with plink finds a majority of SNPs in very high LD
LD
SNP
plink
pruning
1 day ago by
enferdeflame
• 0
0
votes
0
replies
162
views
Difference when using difference number of pathways score to compare between 3 groups
GSVA
Limma
1 day ago by
Chris
▴ 260
0
votes
0
replies
163
views
News:
Online course: Meta-analysis in R
Meta-Analysis
Statistics
R
updated 1 day ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
3
votes
9
replies
703
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 2 days ago by
Elisabeth Gasteiger
★ 2.4k • written 2 days ago by
Jacky
• 0
0
votes
1
reply
239
views
10x VDJ (TCR/BCR) BAM to fastq
TCR
VDJ
BCR
10x
updated 2 days ago by
GenoMax
141k • written 2 days ago by
predeus
★ 1.9k
116,497 results • Page
1 of 2330
Recent Votes
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
Answer: Ubuntu storage space is decreasing automatically
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
The majority of the sequences in Trinity ID do not start from start codons. Can the sequences still be used for primer design and validation?
Answer: Cellranger count error: Input FASTQ file ended prematurely
Answer: RNA seq differential expression analysis
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Recent Replies
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
ATpoint
81k
You can, if you use RStudio via Docker, for example `bioconductor/bioconductor_docker`. I currently manage many different projects with thi…
Comment: bam merging for archaic samples
by
Matteo Ungaro
▴ 100
@Pierre Lindenbaum I see. So, I can actually manipulate just one single RG tag at the time with `samtools`? Which flag should I use, or sho…
Comment: bam merging for archaic samples
by
Pierre Lindenbaum
161k
RG tag "L9302" is missing the the BAM header. You should have something like this in the BAM header ``` @RG ID:L9302 SM:L9302 ``` may be…
Answer: Filtering sam or bam file with maximum matching region
by
Pierre Lindenbaum
161k
> . Is there any way to find through sam or bam file that which chromosomal position are maximum reads aligning to? samtools depth i…
Comment: Calculate Radius of Gyration [python 3]
by
ndm1096
• 0
Hello Franco. I am very much new with bioinformatics but I have been tasked with studying the radius of gyration of a timeseries of a prote…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
That makes a lot more sense. Thank you.
Answer: Removing Illumina microarray probes with no expression HumanHT-12v4
by
Gordon Smyth
★ 7.0k
Type ``` help("read.idat") ``` and read the example at the bottom of the page, which shows you how to set the `other$Detection` component o…
Comment: Free/open source 23andme-like analysis
by
swbarnes2
14k
Accurately assessing a few QC metrics is trivially easy. Assessing the significance of variants in a clinically responsible way is really…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
swbarnes2
14k
If _1 and _2 really are the same library, you should rename the fastqs, or make symlinks, such that they have the same sample name, but dif…
Comment: Cellranger count error: Input FASTQ file ended prematurely
by
ATpoint
81k
Just delete the index read files. They just take up space and will never be used.
Comment: Adding CB tag to bam file
by
swbarnes2
14k
Yes. Why wouldn't you use, say, AddOrReplaceReadsGroups?
Comment: Ciriquant not configuring hisat2 indexed files
by
Atul K.
• 0
Thank you. Decreased the threads to 2 (changed the threads: 2 in the config file; but it was somehow using 4). It did run for sometime but …
Answer: GTF file from Stringtie to R Studio for either Ballgown or DESeq2
by
Ram
43k
See this section on how to use tximport to import StringTie output for DESeq2 processing: https://bioconductor.org/packages/devel/bioc/vign…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Can you explain the normalization or give me a link that describes it, please? Comparison across samples will always be caveated as RNA-seq…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
Sorry, I see how harsh I come across. It's not good practice to use multiple versions of R in the same project. I can understand legacy pro…
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