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9
votes
7
replies
7.2k
views
Align paired and unpaired reads simultaneously using Bowtie2?
alignment
updated 5 days ago by • 0 • written 5.7 years ago by ▴ 20
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
5 days ago by vytarasov ▴ 180
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 6 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
6
votes
7
replies
385
views
Longest transcript variant per gene
transcript longest variant orthofinder
4 days ago by sansan_96 ▴ 90
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 4 days ago by • 0 • written 6.7 years ago by • 0
6
votes
4
replies
13k
views
Trimmomatic: What is the difference between paired and unpaired output files in paired-end mode
trimmomatic paired-end
updated 5 days ago by • 0 • written 6.5 years ago by ▴ 130
6
votes
5
replies
1.7k
views
How to calculate coverage of Nanopore long read data?
sequencing coverage
2 days ago by Arton ▴ 10
5
votes
7
replies
483
views
RNA seq analysis
DESeq RNA-seq
1 day ago by Jacek ▴ 20
4
votes
1
reply
200
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
2 days ago by J. ▴ 40
4
votes
5
replies
4.3k
views
Tool: GRIDSS: the Genomic Rearrangement IDentification Software Suite
Assembly Structural-Variation Variant-Calling
updated 8 hours ago by ▴ 520 • written 7.2 years ago by ★ 2.9k
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv cnvkit exome WES
updated 2 days ago by • 0 • written 5.1 years ago by • 0
4
votes
7
replies
398
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
3 days ago by Chen • 0
3
votes
3
replies
280
views
what is another word for a BLAST "hit"?
blast alignment
6 days ago by dec986 ▴ 380
3
votes
3
replies
357
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 3 days ago by ▴ 140 • written 6 days ago by • 0
3
votes
1
reply
206
views
Question about methylation location
Methylation WGBS bisulfide
updated 6 days ago by ★ 2.0k • written 7 days ago by • 0
3
votes
2
replies
174
views
Details on salmon index
Salmon
updated 16 hours ago by 6.6k • written 23 hours ago by • 0
3
votes
3
replies
221
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm ChIP-seq consensus peaks
updated 23 hours ago by 82k • written 1 day ago by • 0
3
votes
2
replies
189
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 3 days ago by 82k • written 4 days ago by • 0
3
votes
4
replies
329
views
finding evidence(s) of a peptide translated from an "Upstream Open Reading Frame (uORF)"
UTR masspec uORF peptide
updated 19 hours ago by 142k • written 22 hours ago by 161k
3
votes
2
replies
277
views
imputation through beagle
panel beagle reference imputation
3 days ago by analyst ▴ 50
3
votes
3
replies
266
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 3 days ago by 43k • written 17 days ago by • 0
3
votes
7
replies
269
views
Faster Needleman-Wunsch rapid global alignment of two sequences?
Needleman-Wunsch alignment
updated 1 hour ago by ▴ 20 • written 19 hours ago by ★ 2.9k
3
votes
4
replies
318
views
Truncated metadata file report from ENA Portal API
ena python
6 days ago by Giulia • 0
3
votes
6
replies
488
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 4 days ago by ▴ 20 • written 11 days ago by • 0
3
votes
4
replies
245
views
Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer version?
RNA-seq genome
updated 17 hours ago by 43k • written 1 day ago by • 0
3
votes
3
replies
163
views
getting exon coordinates
genomics
updated 17 hours ago by 43k • written 18 hours ago by • 0
3
votes
1
reply
215
views
Long reads and fixing of mate-pair issues/marking duplicates with samtools
mate-pair samtools alignment
updated 3 days ago by ▴ 300 • written 8 days ago by ▴ 40
2
votes
4
replies
218
views
Help with IGV abbreviation
igv
updated 2 days ago by 43k • written 3 days ago by • 0
2
votes
2
replies
162
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell ambient-RNA
updated 12 hours ago by 43k • written 15 hours ago by ▴ 130
2
votes
5
replies
491
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq featureCounts HISAT
updated 2 days ago by 43k • written 8 days ago by • 0
2
votes
3
replies
193
views
ggrepel function: geom_text_repel()
ggplot2 ggrepel R
updated 9 hours ago by 43k • written 1 day ago by ▴ 20
2
votes
2
replies
197
views
Genome Visualization Tools
bacterial genome
updated 2 days ago by 142k • written 2 days ago by ▴ 10
2
votes
5
replies
566
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 4 days ago by ▴ 40 • written 13 days ago by ▴ 30
2
votes
3
replies
272
views
Finding variants within a subset of a BAM file
variant calling
2 days ago by ramiro.barrantes • 0
2
votes
8
replies
375
views
joint callset and vcf sorting, unknown TAG issue
sort bcftools GLNexus merge VCF
updated 4 days ago by 161k • written 4 days ago by ▴ 100
2
votes
3
replies
208
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC RNA-Seq
updated 2 days ago by 43k • written 2 days ago by • 0
2
votes
6
replies
380
views
BWA alignment
Samtools bam
updated 2 days ago by ▴ 260 • written 4 days ago by • 0
2
votes
3
replies
276
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio Cibersort R
3 days ago by Azra ▴ 10
2
votes
6
replies
1.9k
views
How can you *consistently* download BioProject IDs from NCBI's BioSample database using Entrez Direct?
XML ncbi entrez-direct
updated 1 day ago by 43k • written 3.9 years ago by • 0
2
votes
5
replies
266
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 3 days ago by 8.5k • written 3 days ago by • 0
2
votes
4
replies
253
views
Can 5' and 3' scRNAseq be processed with the same pipeline?
singlecell seurat 10XGenomics scRNAseq
updated 1 day ago by ▴ 90 • written 1 day ago by ▴ 20
2
votes
2
replies
178
views
Cannot install bwa-mem2 via conda
conda mamba python
updated 17 hours ago by 43k • written 1 day ago by • 0
2
votes
4
replies
292
views
Benchmarking RNASeq Variant Calling Pipeline (Short Reads)
rna-seq vcf variant-calling
2 days ago by Esraa • 0
2
votes
9
replies
693
views
Filtering Multi-sample VCF file for all except one Genotype
variant SNP VCF
updated 2 days ago by 161k • written 9 days ago by • 0
2
votes
1
reply
232
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 5 days ago by 161k • written 6 days ago by ▴ 70
2
votes
4
replies
5.6k
views
44% Successfully Assigned Fragments with featureCounts after 85% uniquely mapped reads with STAR
rna-seq alignment RNA-Seq featureCounts STAR
updated 3 days ago by ▴ 340 • written 4.9 years ago by ▴ 70
2
votes
0
replies
141
views
Herald: The Biostar Herald for Monday, May 13, 2024
herald
3 days ago by Biostar 2.8k
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 2 days ago by • 0 • written 4.8 years ago by ▴ 60
2
votes
1
reply
258
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
updated 4 days ago by ▴ 210 • written 6 days ago by ▴ 10
2
votes
2
replies
191
views
genome finishing
finishing genome
updated 1 day ago by ▴ 20 • written 1 day ago by • 0
185 results • Page 1 of 4
Recent Votes
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
Answer: ggrepel function: geom_text_repel()
Comment: switch off warning in blast command line
Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
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Recent Replies
Answer: How to handle duplicated genes in TCGA data? by txema.heredia ▴ 130
Having duplicate gene symbols is pretty common. Why do you need to work with gene symbols? To compare them to external datasets? Or just fo…
Comment: Merge clusters in Seurat UMAP by kilcdincer ▴ 10
It did not help either. But I got the answer [here][1] Thank you! [1]: https://github.com/satijalab/seurat/issues/8902
Comment: How to generate table_annovar from VCF input? by Pierre Lindenbaum 161k
there is no `--allsample` option in the "usage" screen you're showing. I suspect you're using an old version ?
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i by egascon • 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem by Pierre Lindenbaum 161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences? by DGTool ▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by b.contreras.moreira ▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Comment: How to generate table_annovar from VCF input? by LucisTheFather • 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU by hophuquy0944 • 0
thank you
Comment: How to extract cells of different species after mapping with combined genome? by Tony • 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Nyksubuz ▴ 10
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test by Nyksubuz ▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
Comment: API kegg - IndexError: list index out of range by Nyksubuz ▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem by saifulislam99121 • 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
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