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91,187 results • Page 1 of 1824
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Job: Research assistant or postdoctoral fellow in computational biology/bioinformatics
computational bioinformatics genomics genetics
18 minutes ago by elimtt • 0
0
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0
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10
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Sequencing depth and raw counts
gene ngs transcriptomics sequencing
30 minutes ago by glady ▴ 270
0
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0
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8
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Job: Multiple Opportunities in Microbial Computational Biology at Lanzatech
Sequence_Analsyis Metagenomics Modeling AI Systems
31 minutes ago by wpmitchell • 0
1
vote
3
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93
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quering publicaly available data sets of RNA-seq and constructing a Kaplan Meier plot
Meier plot Kaplan TCGA cBioportal clinical GDC
updated 44 minutes ago by 6.9k • written 4 hours ago by • 0
0
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1
reply
24
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Possible to remove .nosex IDs in Plink1.9
--allow-no-sex --must-have-sex plink1.9
updated 53 minutes ago by 7.9k • written 2 hours ago by ▴ 20
0
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3
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27
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How to merge variants for the same samples from different vcf files?
vcf
updated 31 minutes ago by 135k • written 1 hour ago by ★ 2.9k
0
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6
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171
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Plink update name flag, setting column names
Plink1.9 --update-name
2 hours ago by salman_96 ▴ 20
7
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9
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6.6k
views
7 follow
Fasta file and GTF file for STAR alignment
STAR ensembl
updated 3 hours ago by 49k • written 2.9 years ago by ▴ 50
2
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2
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57
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Genbank accession number + nucleotide position to genomic coordinates
genbank genome number accession
updated 3 hours ago by 100k • written 4 hours ago by ▴ 10
5
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9
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174
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7 follow
How do I interpret a 200bp reduction of coverage in a gene exon?
readdepth coverage bamfile goldenhelixgenomebrowse
updated 2 hours ago by ★ 1.8k • written 7 hours ago by • 0
0
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3
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65
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Locating BLAST data needed by netsurfp
blast netsurfp
4 hours ago by lefthandgergo ▴ 10
585
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155
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65k
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90 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
handbook tutorial training News
updated 11 days ago by 10 • written 4.4 years ago by 88k
0
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1
reply
27
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Convert phased vcf to Chromosome/scaffold + Tag Haplotype Matrix
vcf phased haplotypes shapeit bcftools
updated 20 minutes ago by ▴ 480 • written 5 hours ago by ▴ 40
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0
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22
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Changes in the definition of resistant, intermediate, and susceptible bacteria
bacteria EUCAST antibiotic_resistance antibiotic
5 hours ago by Negin ▴ 10
4
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4
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90
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UMI deduplication after common sequence (QIAseq miRNA Library Kit)
RNA-seq miRNA UMI
updated 4 hours ago by 100k • written 7 hours ago by • 0
0
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0
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28
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Local database connection and remote download error using curatedTCGAData
TCGA curatedTCGAData bioconductor r
6 hours ago by robjohn70000 ▴ 130
0
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0
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34
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Could bcftools output GQ for homozygous REF call?
samtools gvcf genotype bcftools
6 hours ago by wang.yiguan • 0
0
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0
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41
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MAF and LD matching SNP list
variants snpsnap control
6 hours ago by evol_gen ▴ 70
0
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0
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30
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Resistance breakpoints from CLSI for antibiotic resistance
resistance_cutoffs antibiotic CLSI e._coli
6 hours ago by Negin ▴ 10
0
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0
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31
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How to generate plot with 2 opposite y axis with different scaling?
R Plot
7 hours ago by xqyn • 0
1
vote
7
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199
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How to filter a vcf file based on genotype of first two samples
vcf genotype filter
updated 5 hours ago by 12k • written 1 day ago by ▴ 90
0
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3
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82
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Download whole 1000 genome phase 3 for LD clumping
plink genomic Bioinformatics
updated 4 hours ago by 100k • written 8 hours ago by • 0
0
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1
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63
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Choosing a high soft thresholding power in WGCNA, is it reasonable?
WGCNA
updated 8 hours ago by ★ 1.0k • written 10 hours ago by • 0
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1
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83
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Problem connecting web in PLINK
GWAS PLINK
updated 10 hours ago by 7.9k • written 12 hours ago by • 0
7
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8
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238
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STAR alignment on Windows
RNA-seq STAR
updated 2 hours ago by 9.5k • written 17 hours ago by • 0
0
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2
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64
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GATK error: no positional argument is defined for this tool.
GATK Snakemake
7 hours ago by kamanovae • 0
0
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0
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71
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how to define 15 possible pattern of 5 sequence for tree topology!
unrooted tree topology
11 hours ago by Info.shi ▴ 10
0
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1
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132
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MrBayes Stepping-stone analysis error: DEBUG ERROR: Log likelihood nan after move 'Slider(Ratemultiplier{all})'
stepping-stone mrbayes
11 hours ago by klo • 0
1
vote
4
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878
views
How to determine gender by homozygosity (rate?) in X chromosome?
snp X plink
updated 12 hours ago by • 0 • written 2.1 years ago by ▴ 940
1
vote
1
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190
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Does anyone know if the PCAWG project has a publicly available database on hepatitis B virus integration sites and fusion genes in liver cancer?
hbv pcawg
updated 8 hours ago by ★ 2.0k • written 13 hours ago by ▴ 140
0
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0
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60
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How to put the non-linear regression tendency line to the LD plot?
Linkage SNP Disequilibrium Population
11 hours ago by Manoj ▴ 100
0
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2
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97
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Syntax error in 6 frame translation python code. What is wrong?
Syntax Translations Error Python
1 hour ago by Jager1750 • 0
1
vote
1
reply
101
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Tool: Complex heatmaps
R heatmap customize
updated 8 hours ago by 49k • written 14 hours ago by ★ 11k
0
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3
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171
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Extracting reads from fastq files with BBMAP?
bbmap fastq
updated 13 hours ago by 100k • written 15 hours ago by ▴ 40
3
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10
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218
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HISAT2 Genome indexing
HISAT2 indexing Genome
updated 12 hours ago by ▴ 60 • written 16 hours ago by • 0
0
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0
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43
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Job: Assistant, Associate, or Full Professor in Biological Sciences (Advancing Faculty Diversity)
Neurobio MolecularBio Ecology CellBio Evolution
17 hours ago by lta • 0
0
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0
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49
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Job: Postdoctoral fellow (computational) in Long non-coding RNA (IncRNA) and cancer biology
computational biology Bioinformatics
18 hours ago by EagleEye 6.9k
0
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1
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56
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Building an index using xenome
PDX
updated 4 hours ago by 49k • written 18 hours ago by • 0
0
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0
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34
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Is local ancestry inference usually run with a sequenced reference panel?
rfmix ancestry
19 hours ago by boxate1618 • 0
3
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3
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159
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anybody know what the 4 non-ACGUT characters are in Gencode 38 transcript file, if they do exist?
kallisto gencode.v38.transcripts.fa
updated 19 hours ago by 33k • written 20 hours ago by • 0
0
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2
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95
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Normalization of RNA-seq data with Kallisto/Sleuth for comparisons across treatments
Kallisto Normalization RNA-seq TPM Sleuth
updated 19 hours ago by 33k • written 21 hours ago by • 0
0
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1
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59
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How to do a pairwise alignment and convert the result to a VCF file?
VCF Genomics mutations
updated 20 hours ago by 45k • written 21 hours ago by • 0
0
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0
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36
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bash question: Copy Files to New Directory Using List of File Order
loops bash cli linux command_line
20 hours ago by Simone • 0
3
votes
6
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13k
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Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
ChIP-Seq
updated 20 hours ago by • 0 • written 3.9 years ago by ▴ 370
0
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0
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37
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Is removing rRNAs, tRNAs, etc really a necessary step in the miRNA analysis?
miRNA mirdeep2 gene RNA-seq RNA
21 hours ago by tianshenbio ▴ 110
0
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1
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54
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bedtools intersect combined with filtering after particular word
bedtools
updated 19 hours ago by 33k • written 21 hours ago by • 0
0
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0
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30
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Protein docking and then ligplot
Docking
21 hours ago by samarpitadash93 • 0
0
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2
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68
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cDNA database based on genome resequencing
cDNA resequencing microarray
17 hours ago by boczniak767 ▴ 740
2
votes
2
replies
57
views
[bam-readcount v.0.8.0] Fail to open BAM file –q
bam-readcount BAM file
updated 21 hours ago by 100k • written 21 hours ago by ▴ 10
0
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1
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2.1k
views
vcftools Tajima's D calculation
vcftools tajimasd selection
updated 20 hours ago by 33k • written 17 months ago by ▴ 190
91,187 results • Page 1 of 1824
Recent Votes
Comment: Complex heatmaps
Two Ways To Get Coverage Of Bam But Why Do The Result Is Different?
Does samtools depth know how to handle paired-end reads
Does samtools depth know how to handle paired-end reads
C: Does samtools depth know how to handle paired-end reads
Answer: STAR alignment on Windows
A: Get phylogenetic tree from abundance table
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Recent Replies
Comment: Read MAP and PED files in PLINK by JFeng • 0
Hi, i followed your method and it becomes a rtf file for some reason...Could you explain it in more detail? Thanks!
Comment: Convert phased vcf to Chromosome/scaffold + Tag Haplotype Matrix by 4galaxy77 ▴ 480
Seems like there is a function called hapsFromVCF which is in fineradstructure - did you try that?
Comment: How to merge variants for the same samples from different vcf files? by Pierre Lindenbaum 135k
I'm afraid you need to create and index a tsv file with ` bcftools query` containing the annotations of one of the two files and then use t…
Answer: quering publicaly available data sets of RNA-seq and constructing a Kaplan Meie by EagleEye 6.9k
Hi, For quick overview of your gene-of-interest, protein atlas (in pathology section) includes Kaplan Meier plots for individuals cancer t…
Comment: How to merge variants for the same samples from different vcf files? by steve ★ 2.9k
thanks for the suggestion, but that did not work. It deleted the extra rows instead of merging their INFO and FORMAT values together. So th…
Answer: Possible to remove .nosex IDs in Plink1.9 by chrchang523 7.9k
Two options: 1. Use [--remove][1] on the .nosex file. 2. Download plink 2.0, and use its [--remove-nosex][2] flag. [1]: https://ww…
Answer: How to merge variants for the same samples from different vcf files? by Pierre Lindenbaum 135k
you want bcftools concat with `--remove-duplicates`
Comment: Syntax error in 6 frame translation python code. What is wrong? by Jager1750 • 0
Thank you so much
Comment: Generating consensus sequence from bam file by GenoMax 100k
Use a `-` before `Oz`. Looks like it s missing in the command above. <s>We will confirm and update.</s> Update made.
Answer: Syntax error in 6 frame translation python code. What is wrong? by gb ★ 1.9k
With barely looking at your post, you miss a point before join see https://www.w3schools.com/python/ref_string_join.asp Without testing or…
Comment: STAR alignment on Windows by jared.andrews07 9.5k
I was not aware of that, great point.
Comment: Generating consensus sequence from bam file by a1ultima ▴ 750
Hi @zjamal.msbi19rcms, thanks. I would like to double check what the `Oz` does in the `bcftools norm -f ref.fa Oz -o output.vcf.gz` part. I…
Answer: Plink update name flag, setting column names by salman_96 ▴ 20
Hi, I was able to solve this issue Thank you for help.
Comment: Overall mappability of genome by boczniak767 ▴ 740
Ok, in the end I followed advice on [MACS2 page][1] > usually by taking away the simple repeats and Ns from the total genome, one can get …
Comment: How do I interpret a 200bp reduction of coverage in a gene exon? by Zhilong Jia ★ 1.8k
using PCR to validate the 200bp deletion if the quality of these reads is not very low.
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