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525 results • Page 2 of 11
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0
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5
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312
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Incongruencies in GT assignment by Freebayes
depth freebayes heterozygous genotype
13 days ago by virginia.baraja • 0
0
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5
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279
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How to compare bulk RNA seq data demultiplexed in different ways?
RNA-seq
updated 14 days ago by 43k • written 17 days ago by ▴ 150
0
votes
5
replies
402
views
Error running local blastn in R using system2
blastn NCBI R
20 days ago by Harrison • 0
0
votes
5
replies
485
views
seg fault, core dumped with manta 1.6.0
manta gdb
updated 10 days ago by 43k • written 14 days ago by • 0
0
votes
5
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462
views
Deeptools scale issue for plotHeatmap
deeptools computeMatrix plotHeatmap
27 days ago by Learner • 0
0
votes
5
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372
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 8 days ago by 141k • written 9 days ago by • 0
0
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5
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1.2k
views
RNAseq differential gene expression analysis yield results which come from digestive content
differential-gene-expression RNA-Seq
updated 9 days ago by 43k • written 6.4 years ago by ▴ 90
2
votes
5
replies
344
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats hg002 bed homopolymer-regions
2 days ago by Bikram Kumar • 0
1
vote
5
replies
324
views
samtools filtering
samtools
updated 7 days ago by ★ 1.2k • written 15 days ago by ▴ 80
0
votes
5
replies
361
views
Use of Kraken output for functional analysis
metagenomics kraken shotgun
15 days ago by Srinka ▴ 20
3
votes
5
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394
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity scVelo scRNA-seq splicing
updated 15 days ago by 141k • written 16 days ago by ▴ 190
0
votes
5
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1.6k
views
what does mean this error ? "(ERR): hisat2-align exited with value 1" in mapping long noncoding RNAs
long-non-coding-RNA lncRNA
updated 13 days ago by 43k • written 2.6 years ago by • 0
2
votes
5
replies
657
views
samtools mpileup taking too long
Bam samtools sam alignment
updated 13 days ago by 43k • written 5 weeks ago by • 0
0
votes
5
replies
360
views
Parsing fasta file by coordinates
linux fasta
updated 21 days ago by 141k • written 24 days ago by ▴ 120
5
votes
5
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7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 8 days ago by • 0 • written 3.8 years ago by ★ 1.8k
0
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4
replies
288
views
Questions about transfering wgs file to reference genome file
fasta cram genome
7 days ago by me • 0
1
vote
4
replies
373
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics htseq-count RNA-Seq NGS hisat2
updated 5 days ago by ★ 1.7k • written 7 days ago by • 0
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 1 day ago by 43k • written 5.1 years ago by ★ 2.6k
2
votes
4
replies
271
views
Addmetadata to seurat obj
seurat
8 days ago by synat.keam ▴ 100
1
vote
4
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343
views
Molecular docking with Autodock
Docking proteomics
updated 13 days ago by 43k • written 11 weeks ago by ▴ 10
2
votes
4
replies
371
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 8 days ago by 141k • written 9 days ago by • 0
2
votes
4
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2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 9 days ago by 43k • written 8.0 years ago by ▴ 80
0
votes
4
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389
views
Is it reasonable to discard reads that show variation of quality across its length?
Trimming
21 days ago by BRENO • 0
4
votes
4
replies
348
views
Average expression of a sample in single-cell data
single-cell rna-seq
16 days ago by newuser2024 • 0
0
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4
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2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 24 days ago by • 0 • written 6.5 years ago by • 0
2
votes
4
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1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 15 hours ago by 43k • written 17 months ago by • 0
0
votes
4
replies
1.8k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq batch-effect R
updated 1 day ago by 43k • written 4.8 years ago by ▴ 20
0
votes
4
replies
320
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 7 days ago by 141k • written 10 days ago by • 0
0
votes
4
replies
436
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
3 hours ago by Kai Xin • 0
2
votes
4
replies
295
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP CPU transcriptomics
20 days ago by Mohamed Abderrahmane ▴ 10
1
vote
4
replies
270
views
Removing batch effect using combat-seq
batch effect RNA-Seq combat-seq
updated 17 days ago by ★ 1.7k • written 18 days ago by • 0
0
votes
4
replies
317
views
Compute bootstrap values on consensus tree
phylogeny tree raxml
3 days ago by pablo ▴ 300
3
votes
4
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334
views
Single cell analysis with "meta".tsv.gz file
Single-cell
16 days ago by Estevão • 0
1
vote
4
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2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 1 day ago by 43k • written 4.8 years ago by ▴ 10
0
votes
4
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1.1k
views
Getting biological replicates from SRA run NCBI
fastq AWS SRA RNAseq
17 days ago by Andres ▴ 20
1
vote
4
replies
1.3k
views
Splitting long reads into shorter chunks
long-read
updated 13 days ago by 43k • written 5.8 years ago by ▴ 60
0
votes
4
replies
419
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx deconcolution
1 day ago by feather-W • 0
1
vote
4
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2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 1 day ago by 43k • written 4.7 years ago by ▴ 10
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 15 hours ago by 43k • written 7.1 years ago by ▴ 310
2
votes
4
replies
268
views
SnpEff annotates coding duplication as intronic?
snpeff
2 days ago by kirill.zaslavsky • 0
0
votes
4
replies
303
views
Coverage observed in introns in the Knockdown genes but not in knockout genes
RNA-seq STAR IGV
21 days ago by rohitsatyam102 ▴ 840
0
votes
4
replies
256
views
Adaptive sampling for whole chromosomes
T2T Nanopore AdaptiveSampling aneuploidy centromeres
8 days ago by njornet ▴ 20
1
vote
4
replies
785
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing wgs
9 days ago by Hyper_Odin ▴ 310
1
vote
4
replies
338
views
How to get human-mouse conservation score from UCSC
conservation mouse IGV human score
13 days ago by diqixiaoyaoer ▴ 10
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat CNA Batch-Effect
updated 1 day ago by 43k • written 5.5 years ago by ▴ 150
0
votes
3
replies
203
views
Peptide identification from Mass spec data
Transcriptomics Proteins Mass-spec
updated 14 days ago by 43k • written 14 days ago by ▴ 10
0
votes
3
replies
693
views
PCR duplicates in FFPE RNASeq
PCR-duplicates RNA-Seq FFPE Variant-Calling
updated 23 days ago by 43k • written 21 months ago by ▴ 120
0
votes
3
replies
330
views
How to proceed with downstream analysis after tumor-only snp calling using Varscan2?
snv compressing varscan bcftools
27 days ago by kabir.deb ▴ 80
0
votes
3
replies
256
views
rRNA depletion of RIP-seq samples
rRNA RIP-seq
updated 9 days ago by ▴ 500 • written 9 days ago by • 0
2
votes
3
replies
270
views
Extracting information from my VCF file
VCF
updated 23 days ago by ▴ 40 • written 23 days ago by • 0
525 results • Page 2 of 11
Recent Votes
DNA Methylation: Sequencing Techniques
Comment: How to install Guppy from Nanopore Technologies?
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
Answer: Indexing the Reference Genome is not done in STAR
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi
Comment: Filtration Of Reads With Length Lower Than 30 From Bam
How to compare the quality of assemblies
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Recent Replies
Comment: Adding CB tag to bam file by Maria • 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis by Michael 54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi by Pierre Lindenbaum 161k
> server so I cannot use Blat for this purpose. blat is avilable as a standane tool: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86…
Answer: Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (wi by b.contreras.moreira ▴ 160
My favourite for this task would be [GMAP]( http://research-pub.gene.com/gmap ), which can produce GFF format with option `-f 2`. It is…
Answer: Prediction of Ribosomal RNA Genes Using RNAmmer Software by colindaven 6.3k
Another alternative is the truly free implementation barrnap https://github.com/tseemann/barrnap. This is also installable via conda so qui…
Comment: Filtration Of Reads With Length Lower Than 30 From Bam by Hagen ▴ 10
thanks! This saved me quite some time, I was about to write code to calculate the aligned length from the CIGAR. But this can be done with …
Comment: Per base sequence content failed miserably by Kai Xin • 0
will look into that. Thank you very much
Comment: Korean human genome reference file by SeoGyun • 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool by Ashok • 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo) by cmdcolin ★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB by 航太郎 • 0
Thanks for your guide!
Comment: Removing duplicates by joe ▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis by swbarnes2 14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file by swbarnes2 14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org by Ram 43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
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