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122,211 results • Page 695 of 2445
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4
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2
replies
2.6k
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Extracting specific cancer types from MAF (Mutation Annotation Format) files from TCGA(The Cancer Genome Atlas)
ENCODE mutation maf TCGA cancer
4.7 years ago by peter ▴ 20
0
votes
1
reply
1.1k
views
how to run FATHMM-MKL program based on hg38?
FATHMM-MKL
updated 4.7 years ago by ★ 90k • written 4.7 years ago by ▴ 100
14
votes
26
replies
18k
views
10 follow
makeblastdb Fasta file with 25 sequences gives Error: mdb_env_open: There is not enough space on the disk
blast makeblastdb
updated 4.7 years ago by ▴ 50 • written 5.9 years ago by ▴ 20
0
votes
0
replies
1.7k
views
Job: 2 Computational Biologist / Data scientist positions in single-cell and multi-OMICs data integration at Institut Imagine (Paris, FR)
single-cell sequencing genomics
updated 2.7 years ago by 45k • written 4.7 years ago by ★ 1.8k
2
votes
2
replies
3.7k
views
Question regarding TCGA and TCGAbiolinks --> RNAseq data as HTseq-Counts, FPKM, FPKM-UQ
RNAseq FPKM-UQ FPKM TCGAbiolinks TCGA
4.7 years ago by mario.red8976 ▴ 140
1
vote
1
reply
2.3k
views
Designing linear model matrix (limma) for differential methylation analysis using Illumina EPIC Methylation Array
EPICarray microarray DifferentialMethylation
updated 4.7 years ago by ★ 2.1k • written 4.7 years ago by • 0
0
votes
6
replies
2.0k
views
How do I filter interactions that are more than 100kb and less than 3kb
bed rna genome programming genomics
4.7 years ago by koushikayaluri ▴ 70
3
votes
6
replies
2.1k
views
Selecting genotypes for a specific chromosome belonging to a specific patient from a multi patient VCF file
sequence
4.7 years ago by dk0319 ▴ 70
0
votes
1
reply
934
views
Forum: Apache Spark on AWS
apachespark
updated 4.7 years ago by 23k • written 4.7 years ago by ★ 1.4k
0
votes
8
replies
3.3k
views
MACS: peak calling from snATAC data
ATAC MACS Rstudio Peakcalling
4.7 years ago by abiuma ▴ 30
0
votes
0
replies
849
views
Best way for finding annotated counterparts of unknown transcript after BLAST
blast efetch pipeline annotation
4.7 years ago by Mathias • 0
0
votes
0
replies
3.1k
views
MEGA X (but not MEGA 7) Error: Access Violation loading fasta file
MEGAXError:AccessViolationloadingfastafile
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
2
votes
1
reply
1.5k
views
Bedmethyl
methylation bedmethyl
updated 3.6 years ago by ▴ 120 • written 4.7 years ago by ▴ 50
12
votes
6
replies
11k
views
What do these MA plots signify?
seq rna maplot sequencing deseq2
updated 4.7 years ago by ▴ 170 • written 4.7 years ago by ▴ 10
3
votes
5
replies
2.3k
views
Is there a software for genomic calculation of GC content and Gene density under sliding windows?
GCcontent genedensity
updated 4.7 years ago by 90k • written 4.7 years ago by ▴ 20
1
vote
0
replies
1.4k
views
Combine multiple groups on comparison by edgeR
glm rna-seq edgeR
4.7 years ago by camelest ▴ 50
0
votes
0
replies
677
views
Unable to get root element from XML file
blast galaxy annotation
4.7 years ago by Pamela • 0
7
votes
4
replies
2.7k
views
Per base sequence content of FastQC Report
rna-seq
4.7 years ago by yueli7 ▴ 250
3
votes
3
replies
3.1k
views
How can I get the Shannon and observed alpha diversity Index value?
R
4.7 years ago by dpc ▴ 250
2
votes
5
replies
3.7k
views
Generating a heatmap in DEG analysis
Differential-gene-expression RNA-Seq
updated 19 months ago by 45k • written 4.7 years ago by ▴ 10
0
votes
2
replies
1.5k
views
How can a duplicate read be interchromosomal?
interchromosomal duplicate NGS samtools picard
4.7 years ago by maxrwjones ▴ 60
2
votes
3
replies
4.2k
views
ComplexHeatmap log scale gradient
log colours complexHeatmap
updated 4.7 years ago by 90k • written 4.7 years ago by • 0
6
votes
9
replies
2.9k
views
what can i use many RNAseq data to do ?
RNA-Seq
updated 4.7 years ago by ★ 90k • written 4.7 years ago by ▴ 10
2
votes
4
replies
1.8k
views
bidirectional blast p
Ensembl BLASTpbidirectional orthologus
updated 4.4 years ago by 45k • written 4.7 years ago by • 0
3
votes
2
replies
3.0k
views
UMAP of 10X and SmartSeq2 datasets on same plot
smartseq2 singlecellrna-seq umap 10xgenomics
updated 4.7 years ago by 90k • written 4.7 years ago by ▴ 350
0
votes
1
reply
839
views
Genes IDs of RNA_Seq results
gene format genome fasta conversion
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
0
votes
0
replies
535
views
Figure for relative error with large database
python database
4.7 years ago by Evy_00 • 0
1
vote
0
replies
1.7k
views
Job: Scientific Coordinator / Knowledge Graph Engineer
rdf sparql
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 760
0
votes
5
replies
2.8k
views
How to quickly find the position of k-mer on the genome
alignment sequencing k-mer
updated 3.6 years ago by • 0 • written 4.7 years ago by • 0
4
votes
5
replies
3.0k
views
Bowtie2 & Hisat2 SAM flags above 256?
manual SAM read-mapping flags bowtie2
4.7 years ago by maxrwjones ▴ 60
1
vote
2
replies
1.7k
views
How to get raw read counts of genes/cds/transcripts from SAM/BAM file?
RNA-Seq alignment gene sequencing assembly
4.7 years ago by shail.nair05 ▴ 20
2
votes
4
replies
2.5k
views
How to install Jellyfish in Windows 10?
general
updated 4.7 years ago by ★ 19k • written 4.7 years ago by ▴ 10
0
votes
1
reply
1.1k
views
The effect of metabolomics on other omics
metabolomics multiomics
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 80
0
votes
2
replies
993
views
Figure for relative error with large database
python data
4.7 years ago by Evy_00 • 0
0
votes
0
replies
1.0k
views
LD pruning parameters
linkage pruning plink
4.7 years ago by anithanagaraj93 ▴ 10
0
votes
17
replies
4.3k
views
I am not able to let R read my file
R fasta
updated 4.7 years ago by 3.5k • written 4.7 years ago by • 0
0
votes
1
reply
1.0k
views
Trouble in SNP calling using GATK HaplotypeCaller
gatk genome
updated 4.7 years ago by ▴ 940 • written 4.7 years ago by • 0
4
votes
2
replies
2.3k
views
"heightweight" R-dataset data-structure?
heavyweight R-language
4.7 years ago by natasha.sernova ★ 4.0k
1
vote
2
replies
1.3k
views
How to do clustering of SNPs according to linkage disequilibrium (r2) values?
nex-gen R rna-seq snp genome
3.3 years ago by anikcropscience ▴ 270
0
votes
0
replies
876
views
Getting distance matrix from specific models for AA/Nt MSA
msa distancemodels raxml python biopython
4.7 years ago by Klios3th • 0
0
votes
1
reply
1.4k
views
Altering a python script to calculate GC content
sequence
updated 4.7 years ago by ★ 30k • written 4.7 years ago by ▴ 70
0
votes
0
replies
844
views
Job: Two postdocs (one wet, one dry) in 3' UTR biology and RNA threapeutics
rna machine-learning utr
4.7 years ago by i.sudbery 22k
0
votes
3
replies
2.6k
views
What is the error of this Nexus file? I cannot open it in Figtree
figtree ggtree R phylogenetics
4.7 years ago by fhsantanna ▴ 620
0
votes
3
replies
1.1k
views
Risk calculation in pedigrees
genome
updated 4.7 years ago by ★ 3.0k • written 4.7 years ago by ▴ 30
0
votes
0
replies
667
views
Altering a python script to calculate GC content
sequence
4.7 years ago by dk0319 ▴ 70
0
votes
1
reply
898
views
identify most variable bacteria within microbiome longitudinal data
microbiome longitudinal data statistics R
updated 4.7 years ago by 20 • written 4.7 years ago by ▴ 30
0
votes
0
replies
1.2k
views
How to instsall "Structure 2.3" for windows 10, 64bit
software error
4.7 years ago by hosin • 0
0
votes
1
reply
755
views
Nanopore data error
RNA-Seq
updated 4.7 years ago by 45k • written 4.7 years ago by ▴ 30
0
votes
1
reply
764
views
Having issues with having extra information on my Fasta file.
sequence
4.7 years ago by trejomarco6 • 0
9
votes
5
replies
3.9k
views
Forum: Should I get my MS in Bioinformatics at UCSC or GA Tech
genome
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 10
122,211 results • Page 695 of 2445
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Trimming sequences based on NCBI contamination screen report
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Recent Replies
Answer: Chip-seq analysis Diffbind by ATpoint 90k
I think the results are expected. a) n=2 is underpowered, for any assay and in particular for ChIP-seq which has considerable noise. b) you…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Hi @arup , after changing the file name following the read length, I can process them using cellranger arc successfully. Thank you very muc…
Comment: Visualize methylation status in Pacbio Hifi read by cmdcolin ★ 4.4k
(as the JBrowse dev) I'm glad to hear this. if you see any trouble with it feel free to let me know, I have tried to keep up to date with m…
Comment: low quality data or file name swapping -- cellranger arc errors when processing by Wu-Sheng Zhang ▴ 10
Got it! I will try to switch their name and re-run the cellranger arc. Thank you very much, @arup !
Answer: 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 ▴ 10
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…
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