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122,200 results • Page 662 of 2444
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2
votes
5
replies
9.6k
views
Using Samtools on a Mac terminal
alignment
updated 4.5 years ago by 56k • written 5.2 years ago by ▴ 10
0
votes
1
reply
1.5k
views
Hierarchical clustering using GISTIC 2.0 result
clustering CNV hierarchical GISTIC CNA
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 10
0
votes
4
replies
3.2k
views
How the calculated the decay line by nonlinear regression to the LD plot?
Linkage SNP Disequilibrium Population
4.5 years ago by Kumar ▴ 170
2
votes
5
replies
5.2k
views
MCScanX not read input files
MCScanX synteny blastp gff
updated 4.5 years ago by ▴ 30 • written 7.8 years ago by ▴ 10
0
votes
0
replies
1.2k
views
GSEA error message help: Empty Gene Line
GenePattern GSEA
4.5 years ago by Genosa ▴ 160
3
votes
2
replies
1.8k
views
"orthomcl" python multithreading loading to mysql database table
mysql multiprocessing orthomcl multithreading
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 40
0
votes
1
reply
1.1k
views
how to obtain annotation file from Genbank file
annotation
4.5 years ago by wes ▴ 90
0
votes
0
replies
1.1k
views
Problem plotting GROMACS graphics in xmgrace
grace gromacs md graphic
4.5 years ago by pehenriquejp • 0
0
votes
5
replies
1.8k
views
Protein fasta file header shorten
header shorten fasta
updated 4.5 years ago by ★ 2.9k • written 4.5 years ago by • 0
0
votes
0
replies
682
views
what the orientation of segmental duplications means in UCSC?
duplication segmental
4.5 years ago by greatgene719 ▴ 10
0
votes
3
replies
3.7k
views
What are the columns from pysam fetch?
pysam
updated 4.5 years ago by 22k • written 4.5 years ago by • 0
1
vote
2
replies
1.2k
views
how to download automatically complete genomes with biopython on ncbi
ncbi biopython
updated 2.7 years ago by 45k • written 4.5 years ago by ▴ 20
1
vote
4
replies
1.7k
views
What is the procedure to install tophat
Tophat
updated 4.5 years ago by 154k • written 4.6 years ago by • 0
3
votes
4
replies
2.7k
views
How to merge variants for the same samples from different vcf files?
vcf
4.5 years ago by steve ★ 3.5k
2
votes
3
replies
1.8k
views
download fastq based on fasta file of bacteria genomes
bacteria SNPcalling fastq fasta
4.5 years ago by ali_karimnezhad ▴ 20
4
votes
3
replies
2.0k
views
BioPax vs. OBO and ontologies
obo database ontologies graph biopax
updated 4.5 years ago by ▴ 20 • written 4.6 years ago by • 0
8
votes
4
replies
2.1k
views
rsync/rclone as a snakemake rule
rclone rsync snakemake
4.5 years ago by Ram 45k
1
vote
4
replies
1.5k
views
Tools to translate from proteome to genome and understand genomic data
genome proteome
4.5 years ago by giammafer ▴ 20
3
votes
7
replies
2.3k
views
STAR genome generate error
STAR fastq RNAseq
updated 4.5 years ago by 154k • written 4.6 years ago by ▴ 30
1
vote
1
reply
916
views
Assemble contigs into chromosomes
genome assembly nucmer 10x
updated 4.5 years ago by 16k • written 4.6 years ago by • 0
1
vote
3
replies
3.4k
views
bbduk memory error
bbduk java bbtools memory
updated 4.5 years ago by 45k • written 4.6 years ago by • 0
0
votes
1
reply
1.1k
views
How split regions in half to get at most 1000 bp length?
split linux bedtools R chop
updated 4.6 years ago by 166k • written 4.6 years ago by ▴ 350
1
vote
2
replies
1.4k
views
VarScan2 - fpfilter.pl - failed to get readcounts for variant allele
VarScan2 fpfilter.pl
updated 4.5 years ago by 90k • written 4.6 years ago by ▴ 10
0
votes
2
replies
1.7k
views
DESeq2 + Rsubread: multiple rows for the same transcript ID?? Annotationdbi mapID and select give different results??
rsubread ens.db deseq2 transcriptid annotationdbi
updated 4.5 years ago by 15k • written 4.6 years ago by • 0
1
vote
2
replies
2.9k
views
Determining the PHRED Quality Score
nanopore
4.5 years ago by adhamzul ▴ 20
0
votes
8
replies
2.4k
views
how to find homologous regions using genomic coordinates
homology regions genomic
updated 3.3 years ago by 45k • written 4.6 years ago by ★ 1.3k
0
votes
2
replies
1.2k
views
Online help missing for Populations 1.2.31
phylogenetics vcf Populations phylogeny treemix
4.6 years ago by hemr3 ▴ 10
0
votes
0
replies
848
views
how to match row names of two files quickly using python
python pandas
updated 2.7 years ago by 45k • written 4.6 years ago by ▴ 10
1
vote
1
reply
1.8k
views
single- indexed sequenced as paired end
Chip-seq NGS Illumina
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 20
0
votes
0
replies
738
views
convert genipe *imput2 to plink format
imput2 genipe plink
updated 2.4 years ago by 45k • written 4.6 years ago by • 0
13
votes
8
replies
2.7k
views
Forum: Starting a collective twitter account "Bioinformatician Underhood"
sci-comm
updated 4.4 years ago by 45k • written 4.6 years ago by ★ 3.0k
0
votes
3
replies
1.6k
views
How to interpret min-hash values in phylogeny
phylogeny mash alignment
updated 4.5 years ago by 35k • written 4.6 years ago by ▴ 110
1
vote
2
replies
1.1k
views
basespace data interpretation?
DNA SEQUENCING
4.6 years ago by shweta.johari13 ▴ 30
2
votes
2
replies
1.2k
views
Biologically relevant open reading frame
KO ORF KOZAK BLAST CDS
updated 4.6 years ago by ★ 2.9k • written 4.6 years ago by • 0
0
votes
0
replies
748
views
Tool: Omics Playground Cloud Version
RNA-seq Transcriptomics scRNA-seq Proteomics
4.6 years ago by Axel Martinelli • 0
1
vote
3
replies
3.4k
views
Protein structure validation
Protein homology PROCHECK model
updated 4.5 years ago by ★ 30k • written 4.6 years ago by • 0
1
vote
2
replies
1.4k
views
python
python
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 20
4
votes
5
replies
4.4k
views
How to convert .txt to .vcf?
vcf txt
4.5 years ago by Julia_W • 0
1
vote
2
replies
3.0k
views
Bam File Barcodes and UMIs not Formatted Correctly For Variant Calling
vcf bam scRNAseq variant
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
4
votes
5
replies
3.6k
views
How to create an OTU table out of phyla abundance?
microbiome OTU diversity
updated 4.5 years ago by 3.4k • written 4.6 years ago by ▴ 20
0
votes
1
reply
835
views
Bugs? on GSEA anaylsis
GSEA
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
1
vote
6
replies
9.8k
views
Memory error in python
Protein-Protein Interaction python memory error
updated 4.6 years ago by ▴ 10 • written 5.6 years ago by ▴ 20
0
votes
1
reply
1.8k
views
News: 5th Berlin Summer School in NGS Data Analysis 2021 (October 4-8)
DNA-Seq Workshop RNA-Seq NGS
updated 2.8 years ago by 45k • written 4.8 years ago by 11k
7
votes
3
replies
3.2k
views
dbSNP vcf file is corrupted?
vcf gunzip dbSNP
4.5 years ago by HB ▴ 30
0
votes
3
replies
1.6k
views
blat standalone version won't run in python cgi
BLAT CGI webserver
updated 4.6 years ago by 36k • written 4.6 years ago by • 0
0
votes
1
reply
1.8k
views
How to obtain compile core gene sequences from Roary?
Roary Core genes Pangenomics
updated 4.6 years ago by ▴ 210 • written 5.3 years ago by • 0
0
votes
6
replies
2.2k
views
GTF file procession
ncbi
4.5 years ago by storm1907 ▴ 30
0
votes
2
replies
1.5k
views
Best assembly program for mitochondrion?
mitochondrion assembly mito organelle
updated 4.5 years ago by ▴ 590 • written 4.6 years ago by ▴ 40
1
vote
5
replies
2.2k
views
Group Genes by Protein Coding/Non-coding feature
NON-CODING GENE ID_CONVERSION CODING
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 70
0
votes
2
replies
1.4k
views
basic pathways analysis - bacteria genome
microbial pathway
4.6 years ago by biobiu ▴ 150
122,200 results • Page 662 of 2444
Recent Votes
strong appearing variant not found by haplotypecaller in -ERC mode and deepvariant but with haplotypecaller in normal mode
Answer: How can I easily remove overlapping transcripts, keeping only longest transcript
Answer: Log2 transformation is well used, but is there a good paper that can be used as
Answer: Flatten a GTF
Answer: RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or
Can EdgeR of DeSeq be used for Single-cell RNA-seq?
Answer: Getting the overlap between two GTF files
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Recent Replies
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang • 0
Hi @arup , thank you very much for your suggestions, and here are the results -- they seems correct. May I have your suggestions? Thank you…
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by samuel.a.odonnell ▴ 640
I don't believe merqury ignores softmasked (lower case) nucleotides so I don't think that is the case. From what it sounds like, during th…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thanks a lot to be helpful I’m trying to build a complete `UniProtID` to `GeneSymbol` lookup table and I’m running into a wall. I’ve alrea…
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
thanks for the quick reply. i posted the screenshot. gatk-internally, there is still the difference using -ERC or not, priot is getting …
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by thomas.heigl.ibk ▴ 20
here the igv view. showing the histogram for all samples plus the reads for one: ![enter image description here][1] and expanded view of …
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
Check the read lengths to make sure the files are correct.
Comment: strong appearing variant not found by haplotypecaller in -ERC mode and deepvaria by Pierre Lindenbaum 166k
> Any suggestions or help you could share please, show us an IGV screenshot of the position GATK realign the reads locally, discards read…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
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