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Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
14 minutes ago by J. • 0
0
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0
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11
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Herald: The Biostar Herald for Monday, May 13, 2024
herald
20 minutes ago by Biostar 2.7k
0
votes
1
reply
25
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Splitting Seurat object by sample layers
split seuratobject seurat layers
updated 55 minutes ago by ★ 2.4k • written 1 hour ago by ▴ 10
0
votes
2
replies
29
views
Galaxy StringTie error
stringtie troubleshoot galaxy error
39 minutes ago by trkfs • 0
0
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0
replies
27
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dbNSFP sift scores integration
SIFT VEP dbNSFP
2 hours ago by atariw ▴ 10
0
votes
0
replies
54
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How to interpret infinite odds ratio?
statistics
3 hours ago by Lukas • 0
0
votes
1
reply
76
views
Mouse ribosome sequences in fasta format
fasta mm10 rRNA
updated 3 hours ago by 142k • written 13 hours ago by ▴ 100
0
votes
1
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53
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Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene prediction.
augustus annotation assembly genome
updated 3 hours ago by 8.6k • written 4 hours ago by ▴ 30
0
votes
1
reply
50
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consensus sequence calling
consensus
updated 37 minutes ago by ★ 2.4k • written 4 hours ago by • 0
795
votes
167
replies
143k
views
109 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 3 months ago by 2.7k • written 7.4 years ago by 100k
0
votes
3
replies
94
views
Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log10P value
Seurat R single-cell RNA-seq bioinformatics
5 hours ago by yau • 0
1
vote
1
reply
60
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
updated 1 hour ago by 43k • written 4 hours ago by • 0
0
votes
1
reply
150
views
imputation through beagle
panel beagle reference imputation
updated 4 hours ago by ★ 1.9k • written 2 days ago by ▴ 50
0
votes
0
replies
29
views
Empty kernel in SEACells model
single-cell scanpy seacells python anndata
4 hours ago by JACKY ▴ 140
0
votes
1
reply
308
views
Using samtools with GCS (google cloud storage) on a docker container seems to give "Protocol Not Supported" error
samtools gcs
updated 5 hours ago by ▴ 280 • written 23 days ago by • 0
1
vote
1
reply
150
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair samtools alignment
updated 5 hours ago by ▴ 280 • written 4 days ago by ▴ 40
0
votes
0
replies
48
views
Reference panel of normals for ensembl named refgenome
Mutect2
6 hours ago by gernophil ▴ 80
0
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0
replies
40
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Producing sequence for splicing isoforms
isoform rMATs splicing alternative SplAdder
6 hours ago by tomas4482 ▴ 390
2
votes
3
replies
182
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BWA alignment
Samtools bam
7 hours ago by Vahid • 0
1
vote
2
replies
105
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 7 hours ago by 82k • written 7 hours ago by • 0
0
votes
1
reply
112
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence university assembly protein genomics
updated 8 hours ago by 8.4k • written 1 day ago by • 0
0
votes
1
reply
196
views
Two-Sample Mendelian Randomization: Association between Instrumental Variable and Outcome
Randomization Mendelian two-sample
updated 8 hours ago by ▴ 60 • written 3 days ago by • 0
2
votes
13
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2.8k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 10 hours ago by • 0 • written 4.8 years ago by ▴ 60
0
votes
1
reply
149
views
Generating .bed file and .map file for polyploid vcf file through plink
bed polyploid map plink
updated 11 hours ago by 10k • written 5 days ago by ▴ 50
0
votes
0
replies
64
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lncRNA
tcga lncrna
11 hours ago by jain72744 ▴ 10
0
votes
1
reply
195
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Nomalization - TCGA, RNA-seq and Microarray
TCGA RNA-seq Nomalization Microarray
updated 17 hours ago by ★ 1.2k • written 3 days ago by ▴ 10
2
votes
5
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496
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 23 hours ago by ▴ 40 • written 10 days ago by ▴ 30
1
vote
2
replies
283
views
How to remove multiple batch effects from RNA-seq data before limma differential gene expression analysis?
ComBat-seq limma RNA-seq removeBatchEffect batch-effect
updated 1 hour ago by 43k • written 1 day ago by • 0
1
vote
1
reply
203
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
updated 1 day ago by ▴ 210 • written 2 days ago by • 0
0
votes
2
replies
167
views
Output file of samtools flagstat empty
samtools-flagstat
updated 7 hours ago by 6.4k • written 1 day ago by • 0
0
votes
0
replies
79
views
How can I create a eigencorplot of pca created from deseq2 object with PCAtools
eigencorplot PCAtools deseq2 pca
1 day ago by BioinfGuru ★ 1.7k
2
votes
8
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291
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 1 day ago by 161k • written 1 day ago by ▴ 100
0
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0
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94
views
News: Online course: An Introduction to Nanopore Direct RNA Sequencing
Nanopore RNAseq
1 day ago by carlopecoraro2 ★ 2.5k
0
votes
1
reply
201
views
input file in rmats
rmats
updated 1 day ago by ▴ 120 • written 3 days ago by • 0
2
votes
2
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235
views
Kraken2 database
kraken microbialdb database krakendb kraken2
3 hours ago by Christopher • 0
6
votes
7
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320
views
Longest transcript variant per gene
transcript longest variant orthofinder
21 hours ago by sansan_96 ▴ 90
2
votes
3
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219
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio Cibersort R
6 hours ago by Azra ▴ 10
2
votes
1
reply
195
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 2 days ago by 161k • written 2 days ago by ▴ 70
9
votes
7
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7.1k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 2 days ago by • 0 • written 5.7 years ago by ▴ 20
0
votes
4
replies
338
views
Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in python.
k
8 hours ago by beginner123 • 0
6
votes
4
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13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated 2 days ago by • 0 • written 6.4 years ago by ▴ 130
0
votes
2
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198
views
java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
deducplicated java.nio.bufferunderflowexception haplotypecaller bqsr
9 hours ago by analyst ▴ 50
0
votes
6
replies
358
views
Is it Possible to "Merge" data from Replicates within a VCF SNP File
snp vcf plink bioinformatics genomics
updated 23 hours ago by 161k • written 2 days ago by • 0
0
votes
11
replies
461
views
In IGV is this a heterogeneous mutation or false call?
mutations IGV heterogeneous
21 hours ago by Tuck898 • 0
3
votes
3
replies
240
views
what is another word for a BLAST "hit"?
blast alignment
2 days ago by dec986 ▴ 380
0
votes
1
reply
183
views
extract viral protein of interest from 10k whole viral genomes
nBLAST viral-genome
updated 2 days ago by 43k • written 2 days ago by • 0
0
votes
0
replies
151
views
Marker Features variance by cluster, sample, and treatment group
Seurat scATAC-seq ArchR
updated 2 days ago by 43k • written 3 days ago by • 0
1
vote
3
replies
256
views
How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk vcf liftover
updated 2 days ago by 43k • written 3 days ago by ▴ 260
9
votes
6
replies
12k
views
samtools tview symbols
samtools
updated 8.8 years ago by 12k • written 8.8 years ago by ★ 1.4k
1
vote
7
replies
577
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 3 days ago by 161k • written 6 days ago by • 0
116,901 results • Page 1 of 2339
Recent Votes
Answer: Practical Haplotype Graph v2 not finding correct paths
A: Looking For A Way To Count Total Length Of Regions Of Bed File
The Biostar Herald for Monday, May 06, 2024
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
A: Find consensus overlap between many bed files
Comment: RNA seq analysis
C: What is the best practice of scRNA workflow for multiple patients and samples us
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Recent Replies
Comment: consensus sequence calling by bk11 ★ 2.4k
Please check out these posts https://www.biostars.org/p/367626/
Comment: Galaxy StringTie error by trkfs • 0
will do, thank you
Answer: Splitting Seurat object by sample layers by bk11 ★ 2.4k
You can do the following- Idents(SeuratObj) <- "orig.ident" control_set <- subset(SeuratObj, idents = c("counts.control","data.…
Comment: Galaxy StringTie error by GenoMax 142k
> I have sent a bug report to the Galaxy administrator If you have not done so please post this in Galaxy help forum for directed help: h…
Comment: 44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped by Thind amarinder ▴ 340
Wondering, if it was total RNAseq data? or ployA
Comment: RNA seq analysis by Matthias Zepper 4.6k
It is still obscure to me how many different tissues you would like to include into your comparison and what your intended design is. To …
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred by Juke34 8.6k
You can get a look here https://www.biostars.org/p/9465973/
Answer: Mouse ribosome sequences in fasta format by GenoMax 142k
A version of the mouse rDNA repeat can be found here: https://www.ncbi.nlm.nih.gov/nuccore/BK000964 Use the dropdown menu at top-left t…
Comment: Kraken2 database by Christopher • 0
Hello, Mathew. Firstly, thank you for answering my question. **Sorry, what analysis are you trying to perform with these databases?** I a…
Comment: Benchmarking RNASeq Variant Calling Pipeline (Short Reads) by GenoMax 142k
As long as it is the same GIAB sample you could compare your SNP with the SNP's available for the whole genome set.
Comment: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log by yau • 0
Dear Mensur, Thanks so much for your reply!! In my case, I got 1 control(healthy) and 2 disease mouse Single cell RNA-sew data, so I …
Comment: BWA alignment by ATpoint 82k
The relevant code line is precisely the same as in the question.
Answer: imputation through beagle by dthorbur ★ 1.9k
Building a reference panel from the samples you intend to impute seems like a very circular approach. Plus, GBS is a reduced representation…
Answer: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log by Mensur Dlakic ★ 27k
You seem to have too stringent of a p-value cutoff (1e-5). Hopefully you get the concept of how the interplay of `-log10P-value` and `log2F…
Comment: Single-cell RNA-seq FindMarker and EnhancedVolcano Plot: most genes are low -log by yau • 0
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