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121,230 results • Page
1 of 2425
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Votes
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0
votes
0
replies
25
views
TCGA Germline allelic fraction distribution
calling
variant
tcga
2 hours ago by
ramiro.barrantes
▴ 20
0
votes
2
replies
133
views
Issue in circular heatmap, the rows value are getting interchanged.
R
circos
heatmap
circularheatmap
updated 6 hours ago by
Bastien Hervé
6.3k • written 20 hours ago by
Yukta
• 0
0
votes
2
replies
112
views
STAR alignment not detecting some transcripts / custom reference
star
bwa
rna-seq
alignment
scrna-seq
updated 8 hours ago by
rfran010
★ 1.5k • written 12 hours ago by
npont
• 0
837
votes
170
replies
177k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 25 days ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
0
votes
5
replies
175
views
How to preserve full FASTQ header through alignment and CRAM recovery
bam
fastq
cram
updated 11 hours ago by
GenoMax
151k • written 13 hours ago by
curious
▴ 880
2
votes
3
replies
158
views
No index in the undetermined fastq file
bcl2fastq
13 hours ago by
1769mkc
★ 1.3k
0
votes
3
replies
153
views
error in the output of bedops
human
bedtools
libraries
illumina
bedops
updated 10 hours ago by
GenoMax
151k • written 17 hours ago by
María José
▴ 10
0
votes
3
replies
220
views
RNAseq meta-analysis to identify “consistently expressed” genes
meta-analysis
method
rnaseq
updated 7 hours ago by
rfran010
★ 1.5k • written 1 day ago by
cgibbsm
• 0
0
votes
0
replies
43
views
Job:
Bioinformatician - SAGC at SAHMRI Adelaide, South Australia
Bioinformatician
1 day ago by
Careers@SAHMRI
▴ 50
53
votes
10
replies
56k
views
11 follow
ClusterProfiler : What is GeneRatio and BgRatio?
clusterProfiler
updated 1 day ago by
chong.weelic
• 0 • written 8.6 years ago by
ZheFrench
▴ 590
2
votes
2
replies
433
views
GSEA and Cytoscape Enrichment maps
Cytoscape
RNA-seq
GSEA
updated 1 day ago by
GenoMax
151k • written 10 days ago by
kdca
• 0
3
votes
2
replies
231
views
CNVs annotation after CNVkit and clinical databases
Annotation
CNVs
clinical_database
1 day ago by
AIMAR
▴ 10
0
votes
2
replies
157
views
Proposal on CNV (Copies Variants Numer) analysis tools
Number_Variant
Somatic_data
Help
Copy
1 day ago by
AIMAR
▴ 10
3
votes
0
replies
112
views
Herald:
The Biostar Herald for Thursday, May 22, 2025
herald
1 day ago by
Biostar
3.6k
0
votes
2
replies
161
views
Correcting Technical Artifacts in Cross-Dataset Pseudobulk Analysis
batcheffect
deseq2
pseudobulk
1 day ago by
seojin.yang
• 0
0
votes
1
reply
454
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE
admixture
updated 1 day ago by
pereyra.s
• 0 • written 18 months ago by
maxlaubstein
• 0
0
votes
3
replies
216
views
Remapping assembled contigs from Flye output file
tools
flye
remapping
bioinformatics
aseembly
updated 1 day ago by
GenoMax
151k • written 2 days ago by
synthiiihuh
• 0
2
votes
1
reply
142
views
Where to find hg38 panel-of-normals and germline VCFs without 'chr' prefix?
pon
hg38
vcf
mutect2
gatk
updated 1 day ago by
Pierre Lindenbaum
166k • written 1 day ago by
dpgpfkdkeldi
• 0
0
votes
0
replies
96
views
Contigs Input For Phylogenetic Tree
contigs
phylogeny
nextstrain
phylogenetics
1 day ago by
davidmaimoun
▴ 50
4
votes
3
replies
220
views
assembly tool for plant data
plant
18 hours ago by
analyst
▴ 60
0
votes
0
replies
173
views
Will using different Illumina manifest files (with only chr/position changes) affect genotype calling in GSA microarrays?
Illumina
manifest
microarray
GSA
2 days ago by
windyday
• 0
0
votes
3
replies
231
views
tteximeta problem: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment
teximeta
salmon
updated 1 day ago by
marco.barr
▴ 170 • written 2 days ago by
tarek.mohamed
▴ 370
3
votes
3
replies
285
views
Heatmap of rnaseq data with z-score scale
RNA-seq
updated 2 days ago by
swbarnes2
14k • written 2 days ago by
giovanna
• 0
0
votes
2
replies
235
views
Z-score for scRNA-seq data?
scRNAseq
2 days ago by
S
• 0
0
votes
0
replies
126
views
OncodriveFML warnings
cancer_driver
selection_analysis
driver_genes
oncodrivefml
2 days ago by
yahn
▴ 10
0
votes
2
replies
332
views
European Variation Archive submission eva-sub-cli validation failure: "Sample name concordance check"
eva-sub-cli
EuropeanVariationArchive
submission
database
updated 2 days ago by
Timothee
• 0 • written 3 days ago by
askhat
• 0
0
votes
0
replies
176
views
Job:
Project Research Scientist-I (Bioinformatics – Next Generation Sequencing Data Analysis) - India
Biology
Computational
Bioinformatics
updated 2 days ago by
colindaven
7.5k • written 2 days ago by
Rajunaik Vankudavath
• 0
0
votes
0
replies
143
views
News:
online course: AI for Genomics: from CNNs and LSTMs to TRANSFORMERS
Transformers
CNN
Genomics
LSTMs
AI
2 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
381
views
Anyone familiar with studies on computational neuroscience focused on consciousness, particularly in anatomical areas such as ARAS?
neuroscience
computational
updated 2 days ago by
Bastien Hervé
6.3k • written 3 days ago by
Dun
• 0
0
votes
1
reply
194
views
Evaluating Large CRISPR/Cas9 Deletions (~300 kb) in F0 Xenopus Embryos
CRISPR
large
mosaic
Cas12a
F0
deletion
updated 2 days ago by
GenoMax
151k • written 3 days ago by
Santex
• 0
3
votes
15
replies
669
views
6 follow
Trim CDS to ORF
codon
CDS
offset
transcripts
updated 16 hours ago by
colindaven
7.5k • written 3 days ago by
jaredbernard
▴ 30
1
vote
3
replies
258
views
Multi-omic trajectory on CITE-Seq data
multiomic
10x
single-cell
transcriptomics
trajectory
updated 1 day ago by
ATpoint
88k • written 3 days ago by
firestar
★ 1.7k
10
votes
22
replies
885
views
STAR aligner problem on local laptop
RNA-sequencing
2 days ago by
Morris_Chair
▴ 370
3
votes
8
replies
1.3k
views
Mageck RRA is listing negative controls as high fold change in the gene summary
python
crispr
mageck
updated 3 days ago by
jared.andrews07
★ 18k • written 11 months ago by
liz.b
• 0
0
votes
1
reply
197
views
RNA-seq analysis
STAR
HiSat2
featurecounts
updated 3 days ago by
rfran010
★ 1.5k • written 3 days ago by
SEJAL
• 0
2
votes
2
replies
235
views
Obtaining Q30/Q60 Values from Fastq Files
phred
quality
illumina
rna-seq
updated 3 days ago by
GenoMax
151k • written 3 days ago by
joe_genome
▴ 50
0
votes
1
reply
460
views
Phylogeny aware alignment input
HoSeq
MSA
updated 3 days ago by
zjq6666666
• 0 • written 11 months ago by
Meto
• 0
0
votes
5
replies
369
views
The allele with index 2 is not defined in the REF/ALT columns" error after AF filtering with gnomAD Exome
gnomAD
bcftools
vcf
3 days ago by
erikatatianacs
• 0
1
vote
2
replies
257
views
Drastic drop in RNA-seq read mapping rate when disabling gaps in Bowtie2
bowtie2
updated 3 days ago by
GenoMax
151k • written 3 days ago by
triplee0305
▴ 10
2
votes
10
replies
539
views
RNASeq bulk transcriptomics analysis
RNASeq
Trimgalore
genecounts
STAR
fastqc
updated 1 day ago by
lieven.sterck
15k • written 3 days ago by
rajdeepboral00
▴ 60
0
votes
1
reply
203
views
SSL and Syntax Errors when using fasterq-dump (SRA Toolkit)
sratoolkit
updated 3 days ago by
GenoMax
151k • written 4 days ago by
QURROTU AINI
• 0
0
votes
2
replies
252
views
Download GenomicSEM reference file
GenomicSEM
updated 3 days ago by
1769mkc
★ 1.3k • written 4 days ago by
zhangmyharper
• 0
9
votes
11
replies
559
views
How common is it to split fastq files prior to bwa mem to increase parallelization?
mem
bwa
alignment
updated 1 day ago by
Darked89
4.7k • written 4 days ago by
curious
▴ 880
0
votes
0
replies
175
views
News:
UCSC Xena Webinar Series: Visualize and Analyze Bulk Sequencing Data on Xena
visualization
genomics
cancer
4 days ago by
Mary Goldman
• 0
0
votes
0
replies
182
views
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
normalization
deseq2
host-pathogen
rna-seq
4 days ago by
r-ninja
▴ 20
0
votes
0
replies
179
views
Does vg stats support gaf file?
vg
4 days ago by
Wang Cong
▴ 20
1
vote
1
reply
224
views
Longest Protein per Gene from gpff file
Protein
gpff
updated 4 days ago by
lieven.sterck
15k • written 4 days ago by
reza
▴ 300
2
votes
4
replies
730
views
Modify read groups in BAM file
samtools
BAM
picard
DRAGEN
updated 4 days ago by
jkbonfield
★ 1.3k • written 7 weeks ago by
Alex
• 0
2
votes
1
reply
234
views
Integration of NanoString CosMx FOVs
Spatial
transcriptomics
updated 4 days ago by
Bastien Hervé
6.3k • written 4 days ago by
solo.albif
• 0
1
vote
4
replies
346
views
Bulk RNA-seq differential gene expression analysis on haplotype‑resolved diploid plant assembly
RNA-seq
updated 7 hours ago by
rfran010
★ 1.5k • written 4 days ago by
Zephy
• 0
121,230 results • Page
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Recent Votes
BCL2FASTQ Dual-Index Barcode Collisions - Is the i5 Index not considered when determining the number of mismatches?
BCL2FASTQ Dual-Index Barcode Collisions - Is the i5 Index not considered when determining the number of mismatches?
The Biostar Herald for Thursday, May 22, 2025
Answer: No index in the undetermined fastq file
Answer: No index in the undetermined fastq file
Answer: Trim CDS to ORF
match CpG positions to genes
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Recent Replies
Answer: Issue in circular heatmap, the rows value are getting interchanged.
by
Bastien Hervé
6.3k
Open an issue [here][1] In [circos.heatmap][2] vignette, on the first heatmap, you can guess the row R71 in the block "a". With C10/C9 as …
Comment: How to input INDELs in ped files
by
Mwangana
• 0
@Ant, I have the same issue. Did you successfully resolve it?
Comment: terminal can't activate base automatically (conda)
by
tllee
• 0
I ran into the same problem recently. I tried: conda config --set auto_activate_base true Then I checked the `~/.condarc` file. After…
Comment: How to perform Linkage Disequilibrium (LD) analysis in INDELS
by
Mwangana
• 0
@Ant, you can can convert your data into a VCF file by using VCF-Simplify https://github.com/everestial/VCF-Simplify
Comment: How to perform Linkage Disequilibrium (LD) analysis in INDELS
by
Mwangana
• 0
@dthorbur, I have the same issue. Fortunately my data is in a VCF file. Can you please guide me by outlining the steps how to carryout the …
Comment: RNAseq meta-analysis to identify “consistently expressed” genes
by
rfran010
★ 1.5k
Just adding on, the problem really is that you cannot say if a gene is not expressed just because it's not detected. I think your approach …
Comment: Bulk RNA-seq differential gene expression analysis on haplotype‑resolved diploid
by
rfran010
★ 1.5k
Also, an alternative method would be to quantify gene expression independently of haplotypes and just quantify variant percentage of the ge…
Comment: Bulk RNA-seq differential gene expression analysis on haplotype‑resolved diploid
by
rfran010
★ 1.5k
Yes, I don't think it's too common, but it should fit easily into isoform/allele-aware quantification workflows, no?
Comment: STAR alignment not detecting some transcripts / custom reference
by
rfran010
★ 1.5k
> To debug the source of the problem, I manually aligned my fastq files > to a fasta file containing just the dcm gene using bwa. This repo…
Comment: STAR alignment not detecting some transcripts / custom reference
by
GenoMax
151k
What is this gene supposed to do? Is it being integrated in zebrafish genome and then expected to be expressed? Are there other genes in …
Comment: How to preserve full FASTQ header through alignment and CRAM recovery
by
GenoMax
151k
> I delete FASTQ files after alignment to save space Are you never going to need to submit this data to a resource like SRA? Or do you ha…
Comment: How to preserve full FASTQ header through alignment and CRAM recovery
by
GenoMax
151k
> This seems hacky though Then you can use `reformat.sh` from BBMap suite with option `underscore=t` to convert white space in read names …
Comment: How to preserve full FASTQ header through alignment and CRAM recovery
by
Pierre Lindenbaum
166k
the only tool I know which uses this information is Markduplicate but you can always set a regex to set the fields: https://gatk.broadinsti…
Comment: How to preserve full FASTQ header through alignment and CRAM recovery
by
curious
▴ 880
Thanks. Do people just not worry about keeping individual read barcodes with the alignment? ~97% of my barcodes in the fastq file are ident…
Comment: error in the output of bedops
by
Alex Reynolds
36k
https://github.com/bedops/bedops/issues/287#issuecomment-2904811765
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