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121,903 results • Page 632 of 2439
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0
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5
replies
1.2k
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Find sequence/variants from ancient-DNA genomes
DNA ancient
updated 4.3 years ago by 2.9k • written 4.3 years ago by • 0
4
votes
12
replies
2.7k
views
Multifactor Design For RNA-seq Analysis
Rna-seq batch correction DESeq2 multifactor
4.3 years ago by David Martínez ▴ 10
2
votes
2
replies
1.1k
views
Best hit from BLAST for a particular genomic region
genomic blast region best hit evalue
updated 4.3 years ago by 36k • written 4.3 years ago by ▴ 20
3
votes
4
replies
2.0k
views
Proportion of RNAseq reads mapping to rRNA, tRNA, mRNA, and intergenic or antisense regions of the genome?
GTF featureCounts NGS GFF
updated 4.3 years ago by 22k • written 4.3 years ago by ▴ 80
12
votes
9
replies
7.5k
views
Good annotation databases for a VCF file (somatic variants)
VCF ANNOVAR somatic databases annotation
updated 4.2 years ago by ▴ 130 • written 4.3 years ago by ▴ 110
8
votes
9
replies
2.2k
views
superimpose
discovery ds visualizer
4.3 years ago by Alex ▴ 20
0
votes
2
replies
989
views
X-transposed region on chromosome Y
chromosome-X CNV
updated 2.7 years ago by 45k • written 4.3 years ago by • 0
0
votes
0
replies
622
views
How to run PWM scan with hundreds of PWM at the same time?
PWMScan ATAC-seq PWMtools
4.3 years ago by juanpjlozano • 0
0
votes
7
replies
1.9k
views
How to increase the number of matched sequences in blastn
mismatch blastn
updated 4.3 years ago by ★ 2.9k • written 4.3 years ago by • 0
1
vote
6
replies
2.1k
views
Unable to update Rstudio
updateR
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
0
votes
0
replies
1.6k
views
HOMER annotatepeaks.pl
ChIP-Seq HOMER sequencing next-gen
4.3 years ago by jjp55 ▴ 20
3
votes
4
replies
2.5k
views
6 follow
Segmentation fault in bcftools while changing the sample names
vcftools bcftools
updated 4.3 years ago by 153k • written 4.5 years ago by ▴ 340
3
votes
6
replies
1.9k
views
Convert sam file with no header to fastq
fastq sam gatk
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 80
2
votes
3
replies
1.2k
views
Splice site impact
sites Splice
updated 4.3 years ago by 24k • written 4.3 years ago by • 0
0
votes
3
replies
1.3k
views
mapping with bfast killed when created index
bfast mapping index
updated 4.3 years ago by 13k • written 4.3 years ago by ★ 1.3k
0
votes
1
reply
1.1k
views
How to view large PPI network in STRING database?
PPI large network STRING
updated 4.3 years ago by 27k • written 4.3 years ago by ▴ 80
6
votes
12
replies
5.2k
views
Trim bam file reads to remove all nucleotide over a certain length
bam trimming
updated 4.3 years ago by 153k • written 4.3 years ago by 9.3k
47
votes
22
replies
39k
views
17 follow
Multi-Sample Vcf To Phylogenetic Tree.
vcf
updated 15 months ago by • 0 • written 12.0 years ago by ★ 5.4k
1
vote
2
replies
1.8k
views
bcftools filter
filter bcftools
4.3 years ago by Gregor Rot ▴ 550
0
votes
2
replies
1.6k
views
A USER ERROR has occurred: Bad input: the IUPAC sample specified is not present in the provided VCF file
GATK IUPAC CONSENSUS VCF FastaAlternateReferenceMaker
4.3 years ago by Vanuhi • 0
0
votes
0
replies
591
views
Motif search in protein list
interactome motif search batch
4.3 years ago by florian.roehrig • 0
3
votes
5
replies
2.5k
views
STAR Genome index could not open genomeFastaFile
RNAseq genome alignment STAR
4.3 years ago by bs58 ▴ 10
14
votes
4
replies
4.1k
views
Exclusion Of Regions In Cnv Analysis
plink
updated 3.1 years ago by 45k • written 13.2 years ago by ▴ 60
2
votes
7
replies
1.7k
views
Count the numfer of reads supporting a pattern from a BAM file
samtools
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by ▴ 750
11
votes
2
replies
6.6k
views
OrthoFinder: Diamond or Blast? Which is better?
orthofinder blast sensitivity ortholog
updated 3.5 years ago by ★ 2.9k • written 4.3 years ago by ▴ 190
2
votes
4
replies
2.1k
views
Bray Curtis for functional dissimilarity
dissimilarity bray curtis
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
0
votes
0
replies
673
views
how to use circos plot to plot euchromation and heterochromatin
perl circos plot
4.3 years ago by szp770 ▴ 10
0
votes
0
replies
602
views
Annotations for ReadDepth
CNVs NGS ReadDepth
4.3 years ago by ICfc97 ▴ 20
0
votes
1
reply
2.1k
views
Differential Gene Expression Analysis From TMM normalized counts
RNA-Seq
updated 4.3 years ago by ★ 8.3k • written 6.2 years ago by • 0
9
votes
8
replies
8.3k
views
TMM - Normalized FPKM values for RNASeq data ?
RNA-Seq next-gen R
updated 4.3 years ago by ★ 8.3k • written 9.3 years ago by ▴ 160
2
votes
0
replies
1.0k
views
What rate of heterozygosity is considered low or high in a plant genome assembly?
heterozygosity assembly genome plant
4.3 years ago by resug ▴ 40
1
vote
0
replies
602
views
Full protein sequence or only conserved domains
proteins phylogenetics
4.3 years ago by Vasiliy Krestov ▴ 30
3
votes
1
reply
1.6k
views
canonical transcript from vep
ensembl transcript appris canonical tsl
updated 4.3 years ago by 24k • written 4.3 years ago by ▴ 90
0
votes
0
replies
826
views
DE analysis with Ballgown; what are DE genes produced from data containing three groups
DGE R Ballgown
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
1
vote
1
reply
1.5k
views
What is the correct way of setting the genotype after splitting multi-allelic sites in a VCF file?
genotype bcftools vcf
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 430
0
votes
0
replies
743
views
Nx3 chromosome intrnaction matrix into NxN
matrix hic
4.3 years ago by Oleczkaff • 0
0
votes
2
replies
1.1k
views
Viral taxonomic classification question
taxonomic-classification viral-metagenomics
4.3 years ago by v.berriosfarias ▴ 140
2
votes
3
replies
2.6k
views
Ambiguous SNPs
SNPs
updated 4.3 years ago by 24k • written 4.3 years ago by ▴ 420
0
votes
5
replies
1.4k
views
How to compare pathway significances after treatment?
pathway significance comparison
4.3 years ago by Cancan • 0
2
votes
2
replies
1.2k
views
How to obtain all PDB IDs containing similar binding sites with a specific ligand
protein PDB ligand site binding Binding
4.3 years ago by antoniaa ▴ 30
0
votes
0
replies
886
views
Convert different types of databases to ANNOVAR custom databases
ANNOVAR CIViC DoCM annotation VCF
4.3 years ago by Zahra ▴ 110
4
votes
6
replies
1.7k
views
RNA-seq for beginners
reference resequencing transcriptome gtf sequence gff
4.3 years ago by arko.bmb.du ▴ 20
58
votes
5
replies
30k
views
6 follow
How do you generate TMM normalized counts using EdgeR?
R RNA-seq edgeR
updated 17 months ago by ▴ 70 • written 4.3 years ago by ★ 1.1k
1
vote
5
replies
1.8k
views
filtering dataframe using multiple columns in R
filter R dataframe
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 40
2
votes
5
replies
4.0k
views
Difference between KO and ko numbers?
pathway
updated 4.3 years ago by 3.9k • written 4.3 years ago by ▴ 40
1
vote
1
reply
2.0k
views
How to tell if our ligand-protein docking is good from AutoDock Vina's result
protein-structure vina autodock docking pdb
updated 4.3 years ago by ★ 30k • written 4.3 years ago by ▴ 380
1
vote
5
replies
1.9k
views
How to convert a STK alignment into CLUSTAL?
Boundaries structure RNA
updated 4.3 years ago by ★ 1.1k • written 4.3 years ago by ▴ 80
1
vote
4
replies
1.5k
views
bgr files: change chromosome annotation
sed bedgraph expressions awk
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
0
votes
0
replies
687
views
Cut&Run Matrix Generation
CUTANDRUN CUTANA
4.3 years ago by Mohammed ▴ 10
0
votes
1
reply
757
views
How to handle "no call" on SNP imputation results
GWAS SNP genotype Imputation
updated 4.3 years ago by 89k • written 4.3 years ago by • 0
121,903 results • Page 632 of 2439
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Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
Comment: Is this PCA plot correct??
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Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Thomas.H.Hampton ▴ 10
Thanks again for your carefully considered reply. You asked what I am hoping to learn from a DE analysis. Autologous stem cells are well …
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi ATpoint, thank you very much for the helpful insight! I'm still doing some literature reading on this myself, but have you come across a…
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