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192 results • Page 1 of 4
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13
votes
14
replies
866
views
High Malat-1 expression in single cell data
single-cell
updated 5 days ago by ▴ 40 • written 14 days ago by ▴ 40
10
votes
3
replies
310
views
TFs and Gene databases
Transcription-factor Target Regulatory-Networks
updated 5 days ago by ▴ 180 • written 6 days ago by • 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 6 days ago by 161k • written 5.8 years ago by ▴ 180
10
votes
14
replies
694
views
6 follow
Bacterial plasmid analysis
bacteria plasmid wgs hybridassembly sequencing
updated 6 days ago by 142k • written 12 days ago by • 0
9
votes
23
replies
9.8k
views
Tool: BioLabDonkey - new Mac program for molecular biologists
software biolabdonkey
2 days ago by vytarasov ▴ 180
9
votes
7
replies
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
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation reference panel
updated 3 days ago by ▴ 50 • written 6.4 years ago by ▴ 490
7
votes
1
reply
173
views
Tutorial: removeBatchEffect explained using base R linear models
limma effects batch removebatcheffects
updated 6 days ago by 14k • written 6 days ago by ▴ 360
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 2 days ago by • 0 • written 6.4 years ago by ▴ 130
6
votes
5
replies
2.3k
views
Tophat multiple or unique mapping criteria
RNA-Seq
updated 1 day ago by • 0 • written 6.7 years ago by • 0
6
votes
7
replies
332
views
Longest transcript variant per gene
transcript longest variant orthofinder
1 day ago by sansan_96 ▴ 90
6
votes
2
replies
217
views
EdgeR - relationship between logFC and coefficients
differential-expression r edger
updated 3 days ago by ★ 7.1k • written 4 days ago by ▴ 10
5
votes
5
replies
291
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
6 days ago by Chris ▴ 280
4
votes
7
replies
358
views
How does gene length effect the number of reads mapped
RNA-seq CPM sequencing
4 hours ago by Chen • 0
4
votes
2
replies
258
views
How can I analyze normalized expression data?
DEseq2 RNA-seq
5 days ago by mnx0723 • 0
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 4 days ago by ▴ 180 • written 3.0 years ago by ▴ 20
4
votes
6
replies
1.2k
views
Soft-clipping read ends based on read group
ancient molecule at bam DNA RG ends clipping damage
updated 5 days ago by ▴ 10 • written 2.5 years ago by • 0
4
votes
5
replies
3.4k
views
How to compare compare two Sam files to check mapping
alignment
updated 5 days ago by ▴ 90 • written 6.4 years ago by ▴ 60
4
votes
6
replies
396
views
RNA seq analysis
DESeq RNA-seq
updated 15 hours ago by 4.6k • written 5 days ago by ▴ 10
4
votes
3
replies
2.9k
views
How to solve the error 'ERROR::MATE_NOT_FOUND:Found xxx unpaired mates' when run SamToFastq
samtofasq picard validatesamfile
updated 4 days ago by 161k • written 4 days ago by ★ 1.2k
3
votes
4
replies
295
views
Truncated metadata file report from ENA Portal API
ena python
3 days ago by Giulia • 0
3
votes
3
replies
248
views
Gene Specific coverage from WGS data
WGS SARS-CoV2
updated 6 hours ago by 43k • written 13 days ago by • 0
3
votes
3
replies
294
views
Kraken2 database
kraken microbialdb database krakendb kraken2
updated 4 hours ago by ▴ 130 • written 3 days ago by • 0
3
votes
1
reply
191
views
Question about methylation location
Methylation WGBS bisulfide
updated 3 days ago by ★ 2.0k • written 4 days ago by • 0
3
votes
2
replies
221
views
imputation through beagle
panel beagle reference imputation
11 hours ago by analyst ▴ 50
3
votes
2
replies
139
views
Publish a Letter in higher impact vs Research article in lower impact
Article Letter Journal
updated 19 hours ago by 82k • written 19 hours ago by • 0
3
votes
3
replies
426
views
absolute path for symbolic links in Snakefile
Snakemake
updated 4 days ago by ▴ 770 • written 24 days ago by ▴ 60
3
votes
4
replies
4.0k
views
FarmCPU - how to explain the reported 'effect'?
gwas
updated 5 days ago by • 0 • written 5.5 years ago by 8.5k
3
votes
6
replies
463
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 1 day ago by ▴ 20 • written 8 days ago by • 0
3
votes
3
replies
254
views
what is another word for a BLAST "hit"?
blast alignment
3 days ago by dec986 ▴ 380
2
votes
1
reply
137
views
java out of memory error through beagle for imutation
beagle java.out.of.memory imputation
5 days ago by analyst ▴ 50
2
votes
5
replies
98
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 42 minutes ago by 8.5k • written 4 hours ago by • 0
2
votes
2
replies
176
views
Is therer any suggestions on mapping rate of WGBS data?
mapping read alignment WGBS
6 days ago by Zeng Jingyu ▴ 60
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 14 hours ago by ▴ 340 • written 4.9 years ago by ▴ 70
2
votes
3
replies
210
views
BWA alignment
Samtools bam
19 hours ago by Vahid • 0
2
votes
3
replies
316
views
Problem with Seurat package in PercentageFeatureSet function
cell single
updated 4 days ago by ★ 2.4k • written 8 days ago by ▴ 60
2
votes
5
replies
519
views
Tissue-specific DEG analysis with DEseq2
DEseq2 RNA-seq DEG R
updated 1 day ago by ▴ 40 • written 10 days ago by ▴ 30
2
votes
5
replies
2.5k
views
identifying transgene insertion site in WGS
WGS insertion site trangene de-novo soap
updated 5 days ago by • 0 • written 5.1 years ago by ★ 1.8k
2
votes
3
replies
241
views
error in fun(x((i)), ...) : only defined on a data frame with all numeric alike variables
studio Cibersort R
18 hours ago by Azra ▴ 10
2
votes
1
reply
210
views
Failed to open VCF file
GATK sentieon BWA-MEM
updated 2 days ago by 161k • written 2 days ago by ▴ 70
2
votes
2
replies
228
views
Server or aws cloud- which one is better for gatk pipeline
aws server calling gatk cloud
updated 4 days ago by 54k • written 4 days ago by ▴ 20
2
votes
8
replies
319
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
2
votes
5
replies
380
views
Importing a fastq file
Fastq
updated 4 days ago by ▴ 120 • written 4 days ago by • 0
2
votes
4
replies
716
views
Count all variants from vcf file
variants vcf Count
updated 6 days ago by 161k • written 20 months ago by • 0
2
votes
0
replies
147
views
News: course on Landscape Genomics at the EPFL in Lausanne (June 17-21)
LandscapeGenomics SNPs LocalAdaptation GIS
4 days ago by carlopecoraro2 ★ 2.5k
2
votes
13
replies
2.8k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 22 hours ago by • 0 • written 4.8 years ago by ▴ 60
2
votes
3
replies
211
views
Nextflow: how to get the process work dir, within the process
nextflow
updated 4 days ago by 161k • written 4 days ago by ▴ 10
2
votes
1
reply
233
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome PHG graph
updated 1 day ago by ▴ 210 • written 3 days ago by ▴ 10
1
vote
5
replies
345
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex bwt
updated 5 days ago by 54k • written 6 days ago by • 0
1
vote
4
replies
486
views
cellranger error message
multiplexing cellranger
updated 3 days ago by • 0 • written 3 months ago by ▴ 10
192 results • Page 1 of 4
Recent Votes
A: How can I convert -log10 (p-value) to p-value?
Comment: What does the 'E%' represent in BUSCO results?
Answer: What does the 'E%' represent in BUSCO results?
Answer: Combine Two Affymetrix Datasets With Same Platform
Comment: Kraken2 database
Comment: How does gene length effect the number of reads mapped
Comment: How does gene length effect the number of reads mapped
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Recent Replies
Comment: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
No worries! I found the commit with the maths too: https://gitlab.com/ezlab/busco/-/blame/master/src/busco/busco_tools/hmmer.py?page=2#L135…
Comment: What does the 'E%' represent in BUSCO results? by 林明德 • 0
Thank you for your answer! It really helped me resolve a doubt!
Answer: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
Ah your edit solved this. 50 BUSCOs contain internal stop codons, indicating they might be erroneous gene models, or the genes themselves a…
Answer: MGLTools does not work in windows 11 by Ashfaq • 0
In my case, I did not see iGPU. There is only one option, Intel UHD Graphics. What I need to do?
Comment: What does the 'E%' represent in BUSCO results? by Philipp Bayer 8.5k
funny enough i tried the same thing (i've used BUSCO heaps times but never saw the E:! even the manual lists 'C:89.0%[S:85.8%,D:3.2%],F:6.9…
Comment: What does the 'E%' represent in BUSCO results? by GenoMax 142k
According to ChatGPT: In BUSCO, the "E" category represents "End" or "Endof" gene fragments. These are orthologous groups for which the ge…
Comment: Help with IGV abbreviation by GeneC • 0
Thank you for the link and details
Comment: Help with IGV abbreviation by GeneC • 0
Thank you very much for helping with the details.
Comment: How does gene length effect the number of reads mapped by Chen • 0
thank you :)
Answer: Filtering based on alternate allelic balance by Arton • 0
I found the answer when using bcftools. Is there is a way to do this with FilterVcf? bcftools filter --include '(FMT/AD[0:1])/(FMT/A…
Comment: Help with IGV abbreviation by GenoMax 142k
Those are SAM format fields. Check section 1.4 here: https://samtools.github.io/hts-specs/SAMv1.pdf > 1:2114:12111:13792 That is part of …
Answer: Help with IGV abbreviation by Mathew ▴ 130
Hi, here is a breakdown of each part that you asked about: **flag 99**: This indicates various properties of the read alignment. In this c…
Comment: Kraken2 database by Mathew ▴ 130
I don't see any databases with just pathogenic bacteria genomes from just a quick search, I would imagine that using the Standard-16 databa…
Comment: Galaxy StringTie error by Mathew ▴ 130
I am not sure if this is true for Galaxy, but when I code in Python, SyntaxWarning: invalid escape sequence '' occurs when you want to add …
Comment: Can diamond prepdb be used to make a taxonomically aware database? by GenoMax 142k
Should be possible: https://www.biostars.org/p/430366/ Are you using an older version of `diamond`? Latest versions of `diamond` can use N…
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