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67 results • Page
1 of 2
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Votes
Replies
0
votes
0
replies
5
views
Issues while running blastx
blastx
RNA_seq
1 minute ago by
Foad
▴ 10
0
votes
1
reply
7
views
How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing of the PCR product of 7 housekeeping genes
MLST
phylogenetic
nanopre
updated just now by
Joe
21k • written 12 minutes ago by
Ralph
• 0
0
votes
2
replies
34
views
contrast file in DESeq2 bioconductor
file
DEseq2
contrast
20 minutes ago by
r.shiasi3897
▴ 10
0
votes
1
reply
50
views
Best method for batch correction of three datasets
RNA-seq
updated 22 minutes ago by
ATpoint
78k • written 2 hours ago by
CTLong
▴ 20
0
votes
0
replies
19
views
How to remove 3rd codon positions in a multiple sequence allignment?
i
56 minutes ago by
francesco.degiglio
• 0
0
votes
0
replies
21
views
Classification ML model using different type of data
machine-learning
transcriptomics
R
python
biomarkers
1 hour ago by
sil_bioinfo
▴ 40
0
votes
0
replies
21
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
2 hours ago by
Saad Khan
▴ 420
0
votes
0
replies
31
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
2 hours ago by
Adrian
• 0
1
vote
7
replies
190
views
How to download multiple genome files using command line (MacOS) using datasets
Bacteria
Genome
updated 2 hours ago by
Michael
53k • written 4 hours ago by
scholaraspect2008
• 0
1
vote
1
reply
76
views
GEO dataset Microarray data analysis help
microarray
NCBI
GEO
R
data
2 hours ago by
Confused_human
▴ 20
0
votes
3
replies
118
views
Microarray batch correction method suggestions
microarray
log2_normalized
batch_correction
multiple_datasets
updated 3 hours ago by
ATpoint
78k • written 6 hours ago by
Sumeet
• 0
0
votes
0
replies
47
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
10 hours ago by
Clayton
• 0
0
votes
0
replies
54
views
Enzyme commission number in ncbi Gene database
number
commission
enzyme
10 hours ago by
Maatary
• 0
2
votes
1
reply
113
views
Best way to normalize transcript reads data for PCA & correlation and further biostat analysis
transcript_reads
updated 11 hours ago by
Jeremy
▴ 860 • written 14 hours ago by
Faith
▴ 40
2
votes
2
replies
123
views
Help with gatk CreateSequenceDictionary
GATK
updated 8 hours ago by
GenoMax
136k • written 11 hours ago by
Chris
▴ 230
2
votes
4
replies
246
views
FastQC without yellow box
fastqc
15 hours ago by
lobelino
• 0
0
votes
1
reply
102
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 12 hours ago by
Brian Bushnell
20k • written 15 hours ago by
isMM
• 0
0
votes
0
replies
61
views
error when installing gistic2 using conda
env
gistic2
conda
16 hours ago by
luckyday1661
• 0
0
votes
0
replies
70
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 16 hours ago by
Ram
41k • written 16 hours ago by
boone5jones
• 0
0
votes
0
replies
57
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
16 hours ago by
S
• 0
3
votes
2
replies
198
views
RNA-seq log2 fold change to linear
RNA-seq
DGE
updated 18 hours ago by
jared.andrews07
★ 16k • written 23 hours ago by
hmiller
• 0
74
votes
32
replies
4.8k
views
12 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 16 hours ago by
Ram
41k • written 6 months ago by
Sasha
▴ 770
0
votes
2
replies
158
views
what should I do if I get a compromised sample of scRNA-seq data?
scRNA-seq
data
snRNA-seq
updated 4 hours ago by
ATpoint
78k • written 19 hours ago by
wangjb702
• 0
1
vote
0
replies
74
views
Tool:
De Novo assembler (in C, supports MPI parallelism) available for experimenting with
de-novo
trie
olc
updated 16 hours ago by
Ram
41k • written 19 hours ago by
Graham
▴ 10
0
votes
0
replies
67
views
Comparing 16S rRNA (culture) sequences with metagenome
metagenome
shotgun
rRNA_culture
16S
updated 19 hours ago by
Ram
41k • written 19 hours ago by
aswin
• 0
0
votes
2
replies
140
views
Filling gaps in BAM file
bamtools
samtools
gene
bam
19 hours ago by
hemr3
• 0
0
votes
1
reply
120
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
14 hours ago by
enriquesan
• 0
1
vote
3
replies
188
views
vcftools
vcftools
updated 16 hours ago by
Ram
41k • written 20 hours ago by
sevda
• 0
3
votes
1
reply
116
views
Can't do runPCA after merging a splited Seurat object before UMAP
scRNA-seq
Seurat
updated 19 hours ago by
antonioggsousa
3.0k • written 20 hours ago by
wanaga3166
▴ 10
0
votes
0
replies
64
views
How do I pick the best conditions for scATAC-Seq after a series of bulk test runs?
ATAC-seq
20 hours ago by
cyril-cros
▴ 940
0
votes
1
reply
112
views
Microbial gene coverage from blast result
gene
coverage
5 hours ago by
aanchal.yadav
• 0
0
votes
0
replies
70
views
extracting Uniprot IDs for Kegg pathways
mapping
uniprot
R
kegg
clusterprofiler
22 hours ago by
Assa Yeroslaviz
★ 1.8k
0
votes
3
replies
208
views
GAF files in pangenomics
GO
annotation
updated 1 hour ago by
colindaven
5.8k • written 1 day ago by
Pooja
• 0
2
votes
0
replies
95
views
Herald:
The Biostar Herald for Monday, December 04, 2023
herald
23 hours ago by
Biostar
2.3k
3
votes
3
replies
180
views
how to calculate duplicated reads in single cell RNA 10x genomics data
singlecellRNA
10x-genomics
updated 8 hours ago by
GenoMax
136k • written 1 day ago by
archanaverma433
▴ 10
2
votes
2
replies
167
views
4 Fastq files for a single run generated by 10X
scRNA-Seq
Fastq
SRA
10X
3 hours ago by
hkarakurt
▴ 180
0
votes
3
replies
553
views
How to resolve the error of protein lacking a stop codon when using GenomeThreader for homology prediction?
genome
threader
updated 1 hour ago by
dthorbur
▴ 890 • written 1 day ago by
peanut
• 0
4
votes
6
replies
508
views
6 follow
Forum:
Bioinformatics: what do you think of it in the next 20 years?
future
updated 21 hours ago by
Ram
41k • written 3 days ago by
Daniel
• 0
0
votes
1
reply
219
views
How to convert UNITE dataset into ecoPCR format to perform insilico PCR?
obiconvert
ecoPCR
updated 4 hours ago by
vinranke-adel0j
• 0 • written 6 weeks ago by
shristymaurya012
• 0
9
votes
9
replies
550
views
6 follow
Which language use as a beginner in Bioinformatics and Computational genomics
Computational-genomics
updated 19 hours ago by
Mensur Dlakic
★ 25k • written 2 days ago by
2021ag7698
▴ 10
0
votes
2
replies
200
views
sequencing data from different samples in the Integrative Genome Viewer (IGV)
IGV
VARIANT
updated 19 hours ago by
Ram
41k • written 1 day ago by
José de la Trinidad
• 0
2
votes
3
replies
249
views
Error in blast+
PowerShell
blast
Windows
updated 20 hours ago by
Ram
41k • written 1 day ago by
Alexis
• 0
1
vote
1
reply
182
views
Can't install hisat2 with miniconda
unix
miniconda
hisat2
updated 20 hours ago by
Ram
41k • written 2 days ago by
Ozymandeus
▴ 30
0
votes
2
replies
200
views
RNA seq
Differential-gene-expression
updated 20 hours ago by
Ram
41k • written 1 day ago by
Byonkesh
• 0
1
vote
3
replies
281
views
best BLAST/alignment hits - which criteria is more important?
blast
1 hour ago by
min
• 0
0
votes
1
reply
198
views
Are 10x cellranger-arc ATAC bam files deduplicated?
10x
single-cell
updated 19 hours ago by
Ram
41k • written 3 days ago by
WaterMetal
• 0
5
votes
5
replies
360
views
Using metagenome assembly and binning to identify and mitigate contamination in a genome
genomes
contamination
metagenomics
17 hours ago by
btc347
• 0
0
votes
0
replies
196
views
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
promoter
motif
updated 21 hours ago by
Ram
41k • written 3 days ago by
shome
▴ 10
2
votes
3
replies
283
views
Finding human .vcf files online to download
human
findvcf
vcf
updated 11 hours ago by
cmdcolin
★ 3.4k • written 3 days ago by
eren.idil
▴ 10
0
votes
1
reply
127
views
News:
Course: Genome Assembly and Annotation
Biodiversity
Genome-Assembly
Genome-Annotation
Long-reads
updated 21 hours ago by
Ram
41k • written 4 days ago by
carlopecoraro2
★ 2.4k
67 results • Page
1 of 2
Recent Votes
Answer: BBtools bug in reporting the number of substitutions in the console output, it s
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
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Recent Replies
Comment: How to determine E. coli MLST (Multi Locus Sequence Typing ) from the sequencing
by
Joe
21k
Give the sequences to an MLST server or commandline tool on a per-sample/isolate basis. The tool will specify the format it wants - probab…
Answer: contrast file in DESeq2 bioconductor
by
r.shiasi3897
▴ 10
Thank you very much. i will try it
Answer: Best method for batch correction of three datasets
by
ATpoint
78k
Datasets 1 and 2 have nothing in common to serve as batch correction "anchor" (literally speaking), so you cannot correct for anything here…
Answer: contrast file in DESeq2 bioconductor
by
ATpoint
78k
What do you want to compare? 1) You can compare pairwise, like TS vs EOT and TS vs FU and EOT vs FU. That would be ```r results(dds, c…
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.
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