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206 results • Page
1 of 5
Sort: Votes
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Votes
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74
votes
32
replies
4.8k
views
12 follow
Tool:
ChatGPT optimized for bioinformatics questions
gpt
updated 12 hours ago by
Ram
41k • written 6 months ago by
Sasha
▴ 770
72
votes
27
replies
27k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 1 day ago by
snardeli
• 0 • written 9.8 years ago by
Istvan Albert
99k
16
votes
5
replies
12k
views
Where Can I Find The Basepair Positions Of Chromosome Bands?
chromosome
position
updated 3 days ago by
Malachi Griffith
19k • written 13.2 years ago by
Abdel
▴ 370
12
votes
6
replies
453
views
Problematic fastq files...How can we trust them?
fastq
3 days ago by
blackadder
▴ 30
9
votes
15
replies
816
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
6 days ago by
analyst
▴ 10
9
votes
7
replies
507
views
p-value combination methods
rnaseq
NB-GLM
p-value
meta-Analysis
updated 3 days ago by
Istvan Albert
99k • written 6 days ago by
sehriban.buyukkilic
• 0
9
votes
9
replies
644
views
How to filter .fasta file based on conditional statement
abundance
filtering
fasta
vsearch
4 days ago by
rob_DNA
▴ 20
9
votes
9
replies
538
views
6 follow
Which language use as a beginner in Bioinformatics and Computational genomics
Computational-genomics
updated 15 hours ago by
Mensur Dlakic
★ 25k • written 2 days ago by
2021ag7698
▴ 10
7
votes
14
replies
1.0k
views
Building reference dbSNP file using WGS samples
NGS
WGS
Variant-calling
non-model
Bootstrapping
16 hours ago by
analyst
▴ 10
6
votes
8
replies
497
views
Tools or R / Python packages to perfom ML models
Python
machine-learning
R
transcriptomics
3 days ago by
sil_bioinfo
▴ 40
6
votes
3
replies
249
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 5 days ago by
Jeremy
▴ 860 • written 5 days ago by
ohtang7
▴ 40
5
votes
6
replies
426
views
Generate Read counts from bam file
RNAseq
reference_genome
Deseq2
read_counts
updated 5 days ago by
NextGenSeek
▴ 10 • written 6 days ago by
singhankit973
• 0
5
votes
2
replies
247
views
Fastest way to convert BED to GTF/GFF with gene_ids?
gff
convert
bed
gtf
updated 2 days ago by
cmdcolin
★ 3.4k • written 2 days ago by
alejandrogzi
▴ 110
5
votes
3
replies
297
views
SPAdes error: finished abnormally, OS return value: 21
SPAdes
updated 6 days ago by
Brian Bushnell
20k • written 7 days ago by
jiyoung
▴ 20
5
votes
2
replies
4.4k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
3 days ago by
GenoMax
136k
5
votes
5
replies
356
views
Using metagenome assembly and binning to identify and mitigate contamination in a genome
genomes
contamination
metagenomics
13 hours ago by
btc347
• 0
4
votes
5
replies
897
views
Extracting only soft/hard clipped reads from a bam file
bam
reads
NGS
clipped
data_analysis
updated 4 days ago by
Pierre Lindenbaum
158k • written 14 months ago by
jcn
▴ 30
4
votes
4
replies
315
views
Is there a need to batch correct FPKM or TPM values for within sample comparison
Batch
correction
4 days ago by
CTLong
▴ 20
4
votes
6
replies
495
views
6 follow
Forum:
Bioinformatics: what do you think of it in the next 20 years?
future
updated 16 hours ago by
Ram
41k • written 2 days ago by
Daniel
• 0
4
votes
6
replies
416
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
5 days ago by
cee28
▴ 30
4
votes
5
replies
1.9k
views
How to do simple pathway analysis?
rna-seq
genome
gene
updated 4 days ago by
AK
★ 2.2k • written 4.5 years ago by
Seq225
▴ 110
4
votes
7
replies
306
views
regarding blast result interpretation
blast
updated 5 days ago by
dthorbur
▴ 890 • written 5 days ago by
Raman
• 0
4
votes
3
replies
336
views
GO categorization
Ontology
Gene
updated 3 days ago by
geneontologyhelp
▴ 290 • written 4 days ago by
m.habib
• 0
4
votes
6
replies
447
views
From TPM to raw counts
tpm
Deconvolution
rnaseq
2 days ago by
Gama313
▴ 120
4
votes
0
replies
271
views
Tool:
NOEL: An extremely fast Non-Overlapping Exon Length calculator written in Rust
gene-annotation
exon-length
2 days ago by
alejandrogzi
▴ 110
3
votes
2
replies
210
views
Moving AF tag to new column in a VCF file
mutect2
vcf
6 days ago by
Christian
▴ 30
3
votes
4
replies
319
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 5 days ago by
Nitin Narwade
★ 1.5k • written 6 days ago by
RNAseqer
▴ 250
3
votes
6
replies
450
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 3 days ago by
jv
★ 1.2k • written 5 days ago by
newbee
▴ 40
3
votes
5
replies
522
views
Circular genome browser
genome-browser
circular-genome
updated 6 days ago by
cmdcolin
★ 3.4k • written 4 weeks ago by
giammafer
▴ 20
3
votes
1
reply
201
views
KEGG DATABASE
DATABASE
KEGG
updated 2 days ago by
Mensur Dlakic
★ 25k • written 2 days ago by
Sijjil
• 0
3
votes
4
replies
384
views
Is bisulfite-seq data from different studies comparable with each other?
Methylation
updated 2 days ago by
NextGenSeek
▴ 10 • written 5 days ago by
CTLong
▴ 20
3
votes
3
replies
416
views
How to obtain data on the coordinates of the Exon region from UCSC
hg19
UCSC
exon
3 days ago by
ayasu
• 0
3
votes
2
replies
962
views
How do I download a list of genes involved in cellular metabolism (in humans) based on a Reactome pathway?
genes
metabolism
GO
Reactome
updated 5 days ago by
el24
▴ 40 • written 2.0 years ago by
emmah
• 0
3
votes
2
replies
514
views
BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity
SNP
bbtools
updated 4 days ago by
harold.smith.tarheel
★ 4.9k • written 4 days ago by
Axzd
▴ 50
3
votes
2
replies
295
views
Should I scale all genes in single cell Seurat?
singlecell
3 days ago by
synat.keam
▴ 80
3
votes
2
replies
288
views
Mapping quality in `vg giraffe`
vg
4 days ago by
Wenhai
• 0
3
votes
3
replies
175
views
how to calculate duplicated reads in single cell RNA 10x genomics data
singlecellRNA
10x-genomics
updated 3 hours ago by
GenoMax
136k • written 20 hours ago by
archanaverma433
▴ 10
3
votes
2
replies
648
views
CPTAC data, download, merge
CPTAC
merging
seq
data
RNA
updated 6 days ago by
Mohita
▴ 50 • written 16 months ago by
Rob
▴ 160
2
votes
0
replies
87
views
Herald:
The Biostar Herald for Monday, December 04, 2023
herald
19 hours ago by
Biostar
2.3k
2
votes
1
reply
165
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 6 days ago by
barslmn
★ 2.0k • written 6 days ago by
jiyoung
▴ 20
2
votes
8
replies
1.1k
views
mouse+human cells in 10x scRNA-seq
cellranger
10x
singlecell
updated 17 hours ago by
jared.andrews07
★ 16k • written 14 months ago by
Sy80
▴ 10
2
votes
5
replies
211
views
kallisto index build difference according to version
index
version
kallisto
updated 21 hours ago by
dsull
★ 5.1k • written 23 hours ago by
estilo
• 0
2
votes
1
reply
247
views
EnhancedVolcano underrepresenting DEGs
R
updated 6 days ago by
Kevin Blighe
86k • written 8 days ago by
jabbari.parnian
▴ 30
2
votes
8
replies
744
views
6 follow
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 4 days ago by
ATpoint
78k • written 22 days ago by
ellen.francis
▴ 10
2
votes
4
replies
315
views
How Can I move the scattered dots more closer into the center of box ?
R
Boxplots
geom_jitter
2 days ago by
ohtang7
▴ 40
2
votes
6
replies
6.9k
views
Extracting chimeric reads from mapping
RNA-Seq
alignment
samtools
bwa
updated 5 days ago by
doggie
• 0 • written 6.2 years ago by
Anushka
▴ 20
2
votes
3
replies
718
views
Generate a sequence of specific length with a list of motifs and intersperse with spacers
python
R
perl
motif
sequence
updated 2 days ago by
mopejij688
• 0 • written 2.5 years ago by
rykerklie7
▴ 30
2
votes
2
replies
819
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 6 days ago by
cmdcolin
★ 3.4k • written 6 days ago by
Dylan C-C
• 0
2
votes
2
replies
212
views
R script in docker
R
Visual_studio_code
Docker
4 days ago by
mrashad
▴ 70
2
votes
4
replies
374
views
Human mitochondrial reference genome
reference
genome
mitochondria
6 days ago by
singhankit973
• 0
206 results • Page
1 of 5
Recent Votes
The Biostar Handbook. A bioinformatics e-book for beginners.
GEO dataset Microarray data analysis help
C: Batch effects : ComBat or removebatcheffects (limma package) ?
Answer: Batch effects : ComBat or removebatcheffects (limma package) ?
Answer: Help with gatk CreateSequenceDictionary
Answer: Fastest way to convert BED to GTF/GFF with gene_ids?
Are we tricking ourselves with batch effect correction?
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Adyasha
• 0
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Chris
▴ 230
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Recent Replies
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?
Answer: Best way to normalize transcript reads data for PCA & correlation and further bi
by
Jeremy
▴ 860
Scaling the data will give you Z-scores. This is a standard way of preparing data for PCA. I would also suggest trying a center-log-ratio…
Comment: How to resolve the error of protein lacking a stop codon when using GenomeThread
by
peanut
• 0
Thank you for your answer,but after verifying the protein file, it seems there is no problem. Even if there are missing codons, the program…
Comment: Help with gatk CreateSequenceDictionary
by
Chris
▴ 230
It worked! Thanks Matt!
Comment: Finding human .vcf files online to download
by
cmdcolin
★ 3.4k
i can't really tell you why your code doesn't work if you dont provide it. and, if you describe as much as possible what your goals are, th…
Answer: Help with gatk CreateSequenceDictionary
by
MatthewP
★ 1.3k
maybe try?: -R /variant_calling/Desktop/demo/supporting_files/hg38/hg38.fa -O /variant_calling/Desktop/demo/supporting_files/hg38/hg3…
Comment: Java error while running HiCDC overview code
by
Brian Bushnell
20k
Looks like you have corrupt or improperly-formatted input. It's expecting to parse a floating-point number where the word "score" appears.…
Comment: what should I do if I get a compromised sample of scRNA-seq data?
by
dsull
★ 5.1k
The knee plot is just one type of QC. I'd say just proceed with your analysis and see if you observe anything funky (analysis itself is a Q…
Comment: Annotation GTF/GFF Arabidopsis thaliana
by
enriquesan
• 0
...........
Comment: FastQC without yellow box
by
lobelino
• 0
Thank you for your answer.
Comment: FastQC without yellow box
by
lobelino
• 0
My question is Can I trust the statistics of my data I didn't get any yellow boxes, but I got high media values. Why I didn't get any yello…
Answer: FastQC without yellow box
by
ATpoint
78k
The box is the quartiles, the red line the median. Please google how to read a box plot. Your data is good in terms of base quality.
Comment: FastQC without yellow box
by
Ram
41k
What's your question?<a href="" title="Text added because biostars parser needs it"></a>
Comment: vcftools
by
Ram
41k
Deprecated tools don't just stop producing output/errors, that's now how deprecation works.
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