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1,000 results • Page
1 of 20
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How to remove 3rd codon positions in a multiple sequence allignment?
i
just now by
francesco.degiglio
• 0
0
votes
0
replies
7
views
contrast file in DESeq2 bioconductor
file
DEseq2
contrast
3 minutes ago by
r.shiasi3897
▴ 10
0
votes
0
replies
12
views
Classification ML model using different type of data
machine-learning
transcriptomics
R
python
biomarkers
13 minutes ago by
sil_bioinfo
▴ 40
0
votes
0
replies
11
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
1 hour ago by
Saad Khan
▴ 420
0
votes
0
replies
21
views
Best method for batch correction of three datasets
RNA-seq
40 minutes ago by
CTLong
▴ 20
0
votes
0
replies
13
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
1 hour ago by
Adrian
• 0
1
vote
7
replies
164
views
How to download multiple genome files using command line (MacOS) using datasets
Bacteria
Genome
updated 1 hour ago by
Michael
53k • written 3 hours ago by
scholaraspect2008
• 0
1
vote
1
reply
66
views
GEO dataset Microarray data analysis help
microarray
NCBI
GEO
R
data
2 hours ago by
Confused_human
▴ 20
773
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
0
votes
3
replies
106
views
Microarray batch correction method suggestions
microarray
log2_normalized
batch_correction
multiple_datasets
updated 2 hours ago by
ATpoint
78k • written 5 hours ago by
Sumeet
• 0
0
votes
0
replies
45
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
9 hours ago by
Clayton
• 0
0
votes
0
replies
52
views
Enzyme commission number in ncbi Gene database
number
commission
enzyme
9 hours ago by
Maatary
• 0
2
votes
1
reply
110
views
Best way to normalize transcript reads data for PCA & correlation and further biostat analysis
transcript_reads
updated 10 hours ago by
Jeremy
▴ 860 • written 13 hours ago by
Faith
▴ 40
2
votes
2
replies
121
views
Help with gatk CreateSequenceDictionary
GATK
updated 7 hours ago by
GenoMax
136k • written 11 hours ago by
Chris
▴ 230
2
votes
4
replies
243
views
FastQC without yellow box
fastqc
14 hours ago by
lobelino
• 0
0
votes
1
reply
100
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 11 hours ago by
Brian Bushnell
20k • written 15 hours ago by
isMM
• 0
0
votes
0
replies
56
views
error when installing gistic2 using conda
env
gistic2
conda
15 hours ago by
luckyday1661
• 0
0
votes
0
replies
68
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 15 hours ago by
Ram
41k • written 15 hours ago by
boone5jones
• 0
0
votes
0
replies
56
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
15 hours ago by
S
• 0
3
votes
2
replies
195
views
RNA-seq log2 fold change to linear
RNA-seq
DGE
updated 17 hours ago by
jared.andrews07
★ 16k • written 22 hours ago by
hmiller
• 0
74
votes
32
replies
4.8k
views
12 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 15 hours ago by
Ram
41k • written 6 months ago by
Sasha
▴ 770
0
votes
2
replies
150
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 3 hours ago by
ATpoint
78k • written 18 hours ago by
wangjb702
• 0
1
vote
0
replies
73
views
Tool:
De Novo assembler (in C, supports MPI parallelism) available for experimenting with
de-novo
trie
olc
updated 15 hours ago by
Ram
41k • written 18 hours ago by
Graham
▴ 10
0
votes
0
replies
65
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 18 hours ago by
Ram
41k • written 18 hours ago by
aswin
• 0
0
votes
2
replies
138
views
Filling gaps in BAM file
bamtools
samtools
gene
bam
18 hours ago by
hemr3
• 0
0
votes
1
reply
118
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
13 hours ago by
enriquesan
• 0
1
vote
3
replies
186
views
vcftools
vcftools
updated 15 hours ago by
Ram
41k • written 19 hours ago by
sevda
• 0
3
votes
1
reply
109
views
Can't do runPCA after merging a splited Seurat object before UMAP
scRNA-seq
Seurat
updated 18 hours ago by
antonioggsousa
3.0k • written 20 hours ago by
wanaga3166
▴ 10
0
votes
0
replies
63
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
19 hours ago by
cyril-cros
▴ 940
0
votes
1
reply
109
views
Microbial gene coverage from blast result
gene
coverage
4 hours ago by
aanchal.yadav
• 0
0
votes
0
replies
68
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
21 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
3
replies
206
views
GAF files in pangenomics
GO
annotation
updated 10 minutes ago by
colindaven
5.8k • written 23 hours ago by
Pooja
• 0
2
votes
0
replies
93
views
Herald:
The Biostar Herald for Monday, December 04, 2023
herald
22 hours ago by
Biostar
2.3k
3
votes
3
replies
179
views
how to calculate duplicated reads in single cell RNA 10x genomics data
singlecellRNA
10x-genomics
updated 7 hours ago by
GenoMax
136k • written 23 hours ago by
archanaverma433
▴ 10
0
votes
1
reply
84
views
Funannotate iprscan Creates empty file
funannotate
interproscan
fungus
annotation
23 hours ago by
Umer
▴ 50
0
votes
0
replies
55
views
News:
Online course: Introduction to Python, February 12th-March 11th, 2024
python
courses
1 day ago by
Sole
• 0
0
votes
2
replies
140
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
updated 1 day ago by
rpolicastro
12k • written 1 day ago by
cucindarko51
• 0
0
votes
1
reply
231
views
Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools
softclip
updated 1 day ago by
aw7
▴ 210 • written 4 days ago by
ManuelDB
▴ 80
2
votes
2
replies
158
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
2 hours ago by
hkarakurt
▴ 180
0
votes
3
replies
545
views
How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
genome
threader
updated 40 minutes ago by
dthorbur
▴ 890 • written 1 day ago by
peanut
• 0
4
votes
6
replies
504
views
6 follow
Forum:
Bioinformatics: what do you think of it in the next 20 years?
future
updated 20 hours ago by
Ram
41k • written 3 days ago by
Daniel
• 0
0
votes
1
reply
108
views
Process Truncated fastq file
fastqc
fastq
updated 1 day ago by
GenoMax
136k • written 1 day ago by
waqaskhokhar999
▴ 150
2
votes
5
replies
215
views
kallisto index build difference according to version
index
version
kallisto
updated 1 day ago by
dsull
★ 5.1k • written 1 day ago by
estilo
• 0
0
votes
1
reply
217
views
How to convert UNITE dataset into ecoPCR format to perform insilico PCR?
obiconvert
ecoPCR
updated 3 hours ago by
vinranke-adel0j
• 0 • written 6 weeks ago by
shristymaurya012
• 0
9
votes
9
replies
547
views
6 follow
Which language use as a beginner in Bioinformatics and Computational genomics
Computational-genomics
updated 18 hours ago by
Mensur Dlakic
★ 25k • written 2 days ago by
2021ag7698
▴ 10
1
vote
1
reply
120
views
locuszoom error
locuszoom
updated 1 day ago by
GenoMax
136k • written 1 day ago by
nanodano
▴ 30
0
votes
2
replies
198
views
sequencing data from different samples in the Integrative Genome Viewer (IGV)
IGV
VARIANT
updated 18 hours ago by
Ram
41k • written 1 day ago by
José de la Trinidad
• 0
0
votes
2
replies
507
views
Understanding gene level copy number data from TCGAbiolinks
CNV
TCGA
updated 1 day ago by
Zhenyu Zhang
★ 1.1k • written 13 months ago by
billyK
• 0
2
votes
3
replies
247
views
Error in blast+
PowerShell
blast
Windows
updated 19 hours ago by
Ram
41k • written 1 day ago by
Alexis
• 0
1
vote
3
replies
316
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 1 day ago by
GenoMax
136k • written 1 day ago by
bkffadia
• 0
1,000 results • Page
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Recent Votes
Comment: best BLAST hits - which criteria is more important?
Answer: Can't do runPCA after merging a splited Seurat object before UMAP
Answer: Can't do runPCA after merging a splited Seurat object before UMAP
Answer: RNA-seq log2 fold change to linear
Answer: RNA-seq log2 fold change to linear
Comment: How to download multiple genome files using command line (MacOS) using datasets
Comment: 4 Fastq files for a single run generated by 10X
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Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
by
dthorbur
▴ 890
Ah, there is nothing in your post to suggest you are looking for a specific parameter to ignore a specific warning. I would suggest you edi…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
GenoMax
136k
You can use ./datasets download genome accession --inputfile file_name_w_accession `file_name_w_accession` should contain one access…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
here https://stackoverflow.com/a/1521498 is an example how to use read and for loop, you just need to put in your command.
Answer: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
datasets download genome accession --inputfile accessions.txt --include gff3,gbff,rna,cds,protein,genome,seq-report ---------- Or you…
Comment: GEO dataset Microarray data analysis help
by
Basti
★ 1.9k
First I advise you to take time to correctly edit your post so that your code is readable. Secondly, you provide a lot of irrelevant code l…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
scholaraspect2008
• 0
hi there, thanks for the reply, is it possible to disclose an example of ./datasets script for that? thank you very much. i m currently try…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
Michael
53k
> you can use the commands of curl , wget and slow5curl to download the data from database. Not in this situation, it is much easier to us…
Comment: Microarray batch correction method suggestions
by
ATpoint
78k
Makes no sense in my opinion. It's different experiments that cannot be quantitatively compared.
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
scholaraspect2008
• 0
by means of that, how should i write my scripting? say i have GCF000001 GCF000002 GCF000003 btw sorry if i wasn't that clear with the …
Comment: 4 Fastq files for a single run generated by 10X
by
hkarakurt
▴ 180
Thank you for your detailed answer. I will check the reads and compare them with chemistry manual as you suggested. Thank you again for yo…
Comment: Microarray batch correction method suggestions
by
Sumeet
• 0
Thank you @atpoint for your response. However, aim of analysing to generate a matrix with all dataset available after batch correction.
Comment: what should I do if I get a compromised sample of scRNA-seq data?
by
ATpoint
78k
Agreed. I would just force the cells to 5000 or so, and then proceed with the normal QC. If there's a lot of trash "cells" in the dataset t…
Comment: How to download multiple genome files using command line (MacOS) using datasets
by
rj.rezwan
• 0
you should use the `wild cards` to download all the given above GCF files. Moverover, you can use the commands of `curl` , `wget` and `slow…
Comment: Microarray batch correction method suggestions
by
ATpoint
78k
This has been asked so many times before. Analyse them separately, then make a statement on reproducibility of results using a meta-analysi…
Comment: Microbial gene coverage from blast result
by
aanchal.yadav
• 0
What is qcovhsp (high scoring segment pair) in BLAST output. Can we use this parameter to calculate the gene coverage?
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