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122,201 results • Page 664 of 2445
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15
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10
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13k
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6 follow
STAR alignment on Windows
RNA-seq STAR
updated 4.4 years ago by ★ 2.2k • written 4.6 years ago by ▴ 10
0
votes
2
replies
3.1k
views
GATK error: no positional argument is defined for this tool.
GATK Snakemake
4.6 years ago by kamanovae ▴ 100
0
votes
1
reply
1.2k
views
MrBayes Stepping-stone analysis error: DEBUG ERROR: Log likelihood nan after move 'Slider(Ratemultiplier{all})'
stepping-stone mrbayes
4.6 years ago by klo • 0
1
vote
4
replies
3.7k
views
How to determine gender by homozygosity (rate?) in X chromosome?
chromosome-X plink snp
updated 2.9 years ago by 45k • written 6.7 years ago by ★ 1.4k
1
vote
1
reply
1.3k
views
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 4.6 years ago by ★ 3.0k • written 4.6 years ago by ▴ 250
0
votes
2
replies
1.6k
views
Syntax error in 6 frame translation python code. What is wrong?
Syntax Translations Error Python
4.6 years ago by Jager1750 • 0
2
votes
1
reply
1.3k
views
Tool: Complex heatmaps
R heatmap customize
updated 4.6 years ago by 90k • written 4.6 years ago by ★ 30k
0
votes
3
replies
1.9k
views
Extracting reads from fastq files with BBMAP?
bbmap fastq
updated 4.6 years ago by 154k • written 4.6 years ago by ▴ 130
3
votes
10
replies
3.1k
views
HISAT2 Genome indexing
HISAT2 indexing Genome
updated 4.6 years ago by ▴ 220 • written 4.6 years ago by • 0
0
votes
0
replies
937
views
Job: Assistant, Associate, or Full Professor in Biological Sciences (Advancing Faculty Diversity)
Neurobio MolecularBio Ecology CellBio Evolution
4.6 years ago by UCSDBioSci ▴ 30
0
votes
0
replies
1.1k
views
Job: Postdoctoral fellow (computational) in Long non-coding RNA (IncRNA) and cancer biology
computational-biology
updated 4.4 years ago by 45k • written 4.6 years ago by 7.6k
0
votes
2
replies
1.3k
views
Building an index using xenome
PDX
4.6 years ago by salehm ▴ 10
0
votes
0
replies
789
views
Is local ancestry inference usually run with a sequenced reference panel?
rfmix ancestry
4.6 years ago by boxate1618 ▴ 60
3
votes
3
replies
1.8k
views
anybody know what the 4 non-ACGUT characters are in Gencode 38 transcript file, if they do exist?
kallisto gencode.v38.transcripts.fa
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 20
4
votes
2
replies
3.2k
views
Normalization of RNA-seq data with Kallisto/Sleuth for comparisons across treatments
Kallisto Normalization RNA-seq TPM Sleuth
updated 4.6 years ago by 45k • written 4.6 years ago by • 0
1
vote
2
replies
3.1k
views
How to do a pairwise alignment and convert the result to a VCF file?
VCF Genomics mutations
updated 20 months ago by ▴ 70 • written 4.6 years ago by ▴ 20
0
votes
0
replies
577
views
bash question: Copy Files to New Directory Using List of File Order
loops bash cli linux command_line
4.6 years ago by Simone • 0
5
votes
6
replies
28k
views
Error: Encountered internal Bowtie 2 exception (#1) (ERR): bowtie2-align exited with value 1
ChIP-Seq
updated 4.6 years ago by ▴ 20 • written 8.5 years ago by ▴ 550
0
votes
1
reply
1.2k
views
bedtools intersect combined with filtering after particular word
bedtools
updated 4.6 years ago by 45k • written 4.6 years ago by ▴ 30
0
votes
0
replies
745
views
Protein docking and then ligplot
Docking
4.6 years ago by samarpitadash93 • 0
0
votes
7
replies
2.3k
views
cDNA database based on genome resequencing
cDNA resequencing microarray
4.5 years ago by boczniak767 ▴ 880
3
votes
2
replies
1.2k
views
[bam-readcount v.0.8.0] Fail to open BAM file –q
bam-readcount BAM
updated 2.7 years ago by 45k • written 4.6 years ago by ▴ 10
0
votes
1
reply
9.6k
views
vcftools Tajima's D calculation
vcftools tajimasd selection
updated 4.6 years ago by 45k • written 6.0 years ago by ▴ 210
0
votes
2
replies
967
views
Why does Bowtie2 moidifies reads id?
pysam Bowtie2 fastq
4.6 years ago by papodek ▴ 40
1
vote
2
replies
1.9k
views
Extracting percent identity of mapped reads and the coordinates on the genome the read mapped from a BAM file?
Bedtools PySam python BAM Samtools
4.6 years ago by Eric • 0
1
vote
2
replies
1.3k
views
Strand for GTEx WGS data?
GTEx WGS strand
4.6 years ago by spitzer ▴ 10
0
votes
2
replies
1.2k
views
Corona virus clinical and transcriptome data base
Covid-19 coronavirus database
4.6 years ago by Amir.Asgary ▴ 30
0
votes
2
replies
1.9k
views
two bacteria rna seq mapping using bowtie2 which mode is better end-to-end or local
bacteria bowtie2 rna local end-to-end
4.6 years ago by wang-yanfang • 0
0
votes
0
replies
844
views
Does anyone know how to use an API call to PULL Quality Control (QC) data for sequencing runs on BaseSpace - Illumina Platform
API WGS WES BaseSpace QC
4.6 years ago by screadore ▴ 20
1
vote
2
replies
1.0k
views
need help
microalgae bioremediation CRISPR Cas9
updated 4.6 years ago by 154k • written 4.6 years ago by • 0
0
votes
1
reply
1.7k
views
gnomAD AF = 0 vs gnomAD AF = NA (gnomad V2)
annontation rare genomics variant gnomad
4.6 years ago by jon.klonowski ▴ 210
0
votes
1
reply
802
views
How to color CytoScape nodes with double heatmap?
Heatmap Nodes Color CytoScape
updated 4.6 years ago by ▴ 310 • written 4.6 years ago by • 0
2
votes
3
replies
1.8k
views
Over-representation Gene Ontology Analysis on Subset of DE Genes
GO LRT
updated 4.6 years ago by ★ 19k • written 4.6 years ago by • 0
4
votes
5
replies
3.3k
views
DESeq2 multiple group comparisons
R DESeq2 GeneExpression RNAseq
updated 4.6 years ago by ▴ 390 • written 4.6 years ago by • 0
7
votes
5
replies
6.8k
views
Split SAM file into smaller SAM files by line count
SAM
updated 4.6 years ago by ▴ 30 • written 9.3 years ago by ▴ 60
0
votes
0
replies
542
views
Advice on how to pack software dependencies
dependencies docker conda bash
4.6 years ago by e-nanomsf • 0
12
votes
7
replies
4.4k
views
Why is human genome FASTA file on GENCODE much smaller than that on ENSEMBL?
reference genome GENCODE ENSEMBL
updated 4.5 years ago by 154k • written 4.6 years ago by ▴ 80
0
votes
2
replies
1.2k
views
Annovar Exonic label
annovar
4.6 years ago by Juke34 9.3k
0
votes
0
replies
1.6k
views
Need help in understanding MaxQuant output files
Proteomics
4.6 years ago by rishav513 ▴ 30
2
votes
5
replies
3.4k
views
VEP, dbNSFP, Offline Mode, Cache version
Annotation VEP dbNSFP Ensembl
updated 4.6 years ago by 24k • written 4.6 years ago by ▴ 10
0
votes
4
replies
1.5k
views
InterProScan proxy warning
linux lookup http
4.6 years ago by Sergio • 0
0
votes
0
replies
583
views
Supervised clustering from gene expression (fold change) data
clustering expression supervised
4.6 years ago by nerea.bilbao • 0
0
votes
2
replies
1.8k
views
awk command to print multiple columns
awk
updated 4.6 years ago by 12k • written 4.6 years ago by ▴ 120
1
vote
0
replies
923
views
Gold standard for Mitochondrial DNA variant calling
mitochondrial pipeline NGS
4.6 years ago by Anh ▴ 20
0
votes
0
replies
855
views
Phased SNPs with single rad seq data ?
snp rad single
4.6 years ago by Picasa ▴ 700
2
votes
5
replies
3.2k
views
alignement and Variant calling with BWA and samtools
variant-calling samtools BWA
updated 20 months ago by 45k • written 4.6 years ago by ▴ 30
3
votes
2
replies
2.7k
views
How to convert (Newick) tree topology without branch length!
sed awk perl
updated 4.6 years ago by 22k • written 4.6 years ago by ▴ 30
0
votes
3
replies
2.2k
views
Converting csv or text files to ped and map file for GWAS
plink GWAS
updated 4.6 years ago by 12k • written 4.6 years ago by • 0
0
votes
0
replies
871
views
Job: Postdoc position in computational biology and biochemistry
protein evolution biochemistry
updated 2.7 years ago by 45k • written 4.6 years ago by • 0
3
votes
9
replies
2.8k
views
reference fasta creation
reference mapping fasta
4.6 years ago by geneart$$ ▴ 50
122,201 results • Page 664 of 2445
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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Comment: low quality data or file name swapping -- cellranger arc errors when processing by Arup Ghosh 3.5k
The barcode files with 24nt read length W71_LUNGrep2_S6_L001_R3_001.fastq.gz and W71_LUNGrep2_S6_L002_R3_001.fastq.gz should be the R2.
Comment: ID unifiying across different datasets by GenoMax 154k
Each database has their own method of annotation/validation. Depending on resources available there may be a lag between the databases in t…
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…
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