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121,849 results • Page 401 of 2437
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2
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3
replies
1.8k
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RNASeq data has 3 files R1, R2 and R3, which one is the barcode file?
RNASeq
updated 3.2 years ago by 153k • written 3.2 years ago by ▴ 150
4
votes
3
replies
1.4k
views
Python pandas transforming int to float in gff subsetting
python gff pandas
3.2 years ago by marcela.uliano ▴ 90
0
votes
2
replies
953
views
Plink (1.07 and 1.09) runs and stops after reading map
plink QC GWAS
updated 3.2 years ago by 11k • written 3.2 years ago by ▴ 50
0
votes
8
replies
3.8k
views
mapping reads using kallisto - rna seq analysis
minconda seq analysis rna
updated 3.2 years ago by ★ 2.0k • written 3.2 years ago by ▴ 60
0
votes
1
reply
1.6k
views
3d plot in matplotlib of my own data
matplotlib 3d-graph
updated 3.2 years ago by 45k • written 3.2 years ago by • 0
0
votes
1
reply
1.7k
views
Ligplot plus is not working properly. Help...
binding. chimera. Ligplot. UCSF molecular ligand docking.
updated 3.2 years ago by • 0 • written 3.7 years ago by • 0
4
votes
3
replies
2.8k
views
Tips and tricks for using ImageJ
imageJ macros automation
updated 3.2 years ago by ▴ 930 • written 3.2 years ago by 4.8k
1
vote
2
replies
1.6k
views
scatter plot, gene expression, RNA-seq
RNA-Seq correlation
3.2 years ago by Rob ▴ 180
2
votes
6
replies
1.5k
views
how to move files into samples.txt
samplestxt
updated 3.2 years ago by 153k • written 3.2 years ago by ▴ 10
3
votes
2
replies
3.4k
views
How to fix phenotype information when converting from VCF to PLINK
GWAS QC Phenotype PLINK VCF
updated 3.2 years ago by • 0 • written 4.1 years ago by ▴ 30
0
votes
1
reply
797
views
Tools for functional annotation of nucleotide and amino acid sequences ?
gene genome protein
updated 3.1 years ago by ▴ 30 • written 3.2 years ago by ▴ 1000
0
votes
0
replies
597
views
Is it normal that my amplicon sequence variants (ASVs) have gaps ?
ASVs DADA2 fasta
3.2 years ago by v.berriosfarias ▴ 140
1
vote
3
replies
1.2k
views
Hisat2 Script Help
hisat2 mapping
updated 2.5 years ago by 45k • written 3.2 years ago by ▴ 10
0
votes
1
reply
734
views
kallisto/deseq2 - quantifying viral RNA reads and mouse transcriptome at the same time
kallisto deseq2
updated 3.2 years ago by 5.0k • written 3.2 years ago by ▴ 10
4
votes
4
replies
3.3k
views
distinguishing PCR and optical duplicates
Picard Illumina Clumpify duplicates
updated 3.1 years ago by 153k • written 3.2 years ago by ▴ 30
2
votes
1
reply
4.3k
views
How to use minimap2?
sequencing indexing minimap2 read-mapping
updated 3.2 years ago by 153k • written 3.2 years ago by ▴ 20
2
votes
3
replies
1.6k
views
Include DEGs with a -l2fc in overrepresentation analysis?
gene log Overrepresentation fold set DEGs changes analysis
updated 3.2 years ago by ★ 8.3k • written 3.2 years ago by ▴ 10
2
votes
1
reply
1.5k
views
Input problem with EIGENSTRAT
eigenstrat
updated 3.2 years ago by 2.9k • written 3.2 years ago by ▴ 380
0
votes
2
replies
1.7k
views
Unable to install "DESeq2"(annobin.so : No such file or directory)
Linux R Fedora
updated 3.2 years ago by ▴ 30 • written 3.5 years ago by • 0
0
votes
8
replies
2.4k
views
How to convert gene IDs to gene symbols in R?
gene R PCA IDs
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 180
2
votes
2
replies
918
views
How to insert quotes around description of format field in vcf header?
vcf bcftools
3.2 years ago by Alewa ▴ 190
0
votes
1
reply
2.7k
views
software to caculate gene frequency based on SNP ped and map file
SNP genotype
updated 3.2 years ago by 5.0k • written 10.4 years ago by ▴ 150
1
vote
2
replies
1.9k
views
FastaAlternateReferenceMaker is not outputting fasta sequence for multiple samples from a VCF
GATK SNP fasta sequence alignment
3.2 years ago by anikcropscience ▴ 270
3
votes
7
replies
4.2k
views
Tabix '[E::get_intv] Failed to parse TBX_VCF' error
vcf tabix
updated 3.1 years ago by 3.1k • written 3.2 years ago by ▴ 100
1
vote
4
replies
1.5k
views
PHG Imputation
PHG Keyfile Imputation
updated 3.2 years ago by ▴ 420 • written 3.2 years ago by ▴ 20
3
votes
2
replies
1.4k
views
Biomart doe not convert between RefSeq and Ensembl Transcripts in GRCh37?
Transcripts Ensembl GRCh37 RefSeq
3.2 years ago by Manuel ▴ 50
8
votes
13
replies
5.9k
views
7 follow
error while testing nextflow with --genome GRCh38
java nextflow
updated 23 months ago by • 0 • written 3.2 years ago by ▴ 520
0
votes
2
replies
1.1k
views
Metagenome Assembly
taxonomy Assembly Binning Metagenomics
3.1 years ago by serene.s • 0
0
votes
0
replies
738
views
SURVIVOR bed file
BED CNV SURVIVOR VCF
updated 2.5 years ago by 45k • written 3.2 years ago by • 0
3
votes
2
replies
1.6k
views
Filtering AA sequences of PDB structures by sequence identity
identity python sequence
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 70
0
votes
6
replies
1.9k
views
How can I get the positions where a sequence was aligned as output of a pair-wise alignment?
R pair-wise alignment
updated 3.2 years ago by 5.1k • written 3.2 years ago by ▴ 10
2
votes
5
replies
2.1k
views
Excluding an organism in biopython BLAST
biopython blast
updated 3.2 years ago by 153k • written 3.2 years ago by • 0
0
votes
0
replies
461
views
Transcribed Strand vs Non-transcribed strand (TS vs NTS) and bedtools coverage
bedtools
updated 2.2 years ago by 45k • written 3.2 years ago by • 0
2
votes
3
replies
1.3k
views
The difference of RNA-seq data between TCGA and ENCODE
RNA-seq
updated 3.2 years ago by ★ 4.4k • written 3.2 years ago by • 0
0
votes
0
replies
627
views
EdgeR and isoform/allele specific differential expression analysis
RNAseq edgeR rpvg isoform alleles
3.2 years ago by lsoldini • 0
0
votes
3
replies
835
views
Help on Oncomine VCF file "ID" nomenclature
VCF RNAseq
updated 3.2 years ago by 166k • written 3.2 years ago by • 0
2
votes
1
reply
1.1k
views
Good statistics for RNA-seq alignments using RSEM
cnt rsem stat rsem-calculate-expression alignment
updated 3.2 years ago by ★ 2.0k • written 3.2 years ago by • 0
0
votes
8
replies
2.5k
views
Set up conda rna seq analysis
seq conda analysis rna
3.2 years ago by bioinformatics ▴ 60
0
votes
2
replies
861
views
Remote connection using GUI versus terminal on Mac
connection server remote to
updated 3.2 years ago by 22k • written 3.2 years ago by • 0
0
votes
1
reply
781
views
Software to produce position-specific conservation of multiple sequence alignment results?
transcriptomics genomics alignment proteomics
updated 3.2 years ago by ★ 29k • written 3.2 years ago by ▴ 750
0
votes
0
replies
628
views
News: Final Call! Tomorrow (7/8) is the Deadline for Phase 1 submissions of the NCTR Indel Calling from Oncopanel Sequencing Data Challenge!
oncopanel indel-calling
updated 2.7 years ago by 45k • written 3.2 years ago by ▴ 10
1
vote
4
replies
1.5k
views
Count multi range + Same Column
python Excel
updated 3.2 years ago by ▴ 840 • written 3.2 years ago by ▴ 10
0
votes
1
reply
668
views
Similarity measures for networks with same nodes
networks GRNs graphs
updated 3.2 years ago by 5.0k • written 3.2 years ago by • 0
0
votes
0
replies
581
views
Convert Recombination txt file to Plink format
plink recombination map genetic
3.2 years ago by nanodano ▴ 30
0
votes
2
replies
1.5k
views
How to bring in Processed GEO Data ((scRNA-seq) into R and convert into Seurat Object for analysis ?
Seurat GEO RNA-seq
updated 3.2 years ago by 153k • written 3.2 years ago by • 0
1
vote
1
reply
882
views
enrichGO results
clusterProfiler enrichGO
3.2 years ago by Shakiba ▴ 20
1
vote
1
reply
942
views
cnetplot and barplot don't show top ranked GO enrichments.
barplot Goenrichment cnetplot
updated 3.2 years ago by 45k • written 3.2 years ago by ▴ 20
0
votes
1
reply
1.2k
views
Accessing expression matrix for particular cell/feature in Seurat (R)
scRNA r seurat R Seurat
updated 3.2 years ago by ★ 1.9k • written 3.2 years ago by ▴ 40
0
votes
4
replies
1.7k
views
Running Docker Container Built on GNU Guix on a Mac OS
OS Docker GNU Guix Container Mac Minimap2
3.2 years ago by f.wu • 0
0
votes
8
replies
1.5k
views
Combine metadata
python metadata genome
updated 3.2 years ago by 45k • written 3.2 years ago by ▴ 170
121,849 results • Page 401 of 2437
Recent Votes
C: How To Split A Bam File By Chromosome
DESeq2 time-series - full model matrix is less than full rank
Answer: RNAseq requirements: Biological and Technical replicates
C: Differential Peaks Between Replicates
Answer: DESeq2 time-series - full model matrix is less than full rank
Answer: DESeq2 time-series - full model matrix is less than full rank
Answer: Tools for raw reads that estimate the percentage of reads that hit marker genes
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Recent Replies
Comment: Reading AD and other genotype information from the VCF file by Pierre Lindenbaum 166k
`bcftools query -f '[%CHROM %POS %REF %ALT %SAMPLE %GT %AD\n]' `
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes by colindaven 7.8k
This one has the massive computing resources at the EBI behind it, so I wouldn't worry about capacity. Check their stats.
Answer: Cibersortx server down? by GenoMax 153k
Yes it is down now (though it was working ~ 3-4 hours ago): https://downforeveryoneorjustme.com/cibersortx.stanford.edu?proto=https
Answer: Available signature matrix for deconvoluting my bulk data using CIBERSORTX by Sam • 0
Have you checked out [cellxgene][1]? If you filter by organism you might find one that is suitable. [1]: https://cellxgene.cziscience.c…
Comment: RNAseq requirements: Biological and Technical replicates by jkim ▴ 220
Ouch, my mistake. Updated my comment.
Comment: RNAseq requirements: Biological and Technical replicates by i.sudbery 22k
However, one might argue that multiple biological samples (i.e. multiple blood draws) from each patient might be useful. Still, probably no…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes by Mensur Dlakic ★ 29k
> So maybe this approach will help us find interesting and rare pathways — something along those lines. Still the same answer as before - …
Comment: ATAC-seq fragment size distribution - huge spike at 150 bp by yuntan1992 • 0
or add parameter "--soft-clipped-unmapped-tlen"
Comment: CIBERSORTx error: 'x' must be an array of at least two dimensions by ATpoint 89k
I would take this opportunity to encourage using different tools. Cibersortx is not open, its source code has never been published. That ha…
Answer: CIBERSORTx error: 'x' must be an array of at least two dimensions by catarinaventura_pt • 0
For those still looking for the answer about this, I just figured out that you need to have replicates for it to work.
Comment: CIBERSORTx error: 'x' must be an array of at least two dimensions by catarinaventura_pt • 0
I´m having the same problem here described. Any updates on how to solve this?
Answer: ATAC-seq fragment size distribution - huge spike at 150 bp by yuntan1992 • 0
After removing adapters with trim_galore, change the parameter of bowtie2 " --local" to "--end-to-end".
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes by shevch2009 ▴ 20
That is a great comparison! :) It definitely looks that way. :) It's not about taxonomy, but about reconstructing metabolic pathways direc…
Comment: How to connect the UCSC when i get the DMR.plot? by Wren • 0
I tried using the main site but it still didn't work. Thanks anyway, I'll try other methods.
Answer: Tools for raw reads that estimate the percentage of reads that hit marker genes by Mensur Dlakic ★ 29k
If you want an overall taxonomic profile, this tool will do it from reads directly: https://github.com/DessimozLab/read2tree > Well, …
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