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121,896 results • Page 672 of 2438
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6
votes
11
replies
3.9k
views
Download all Bacteria accession list from NCBI
number accession NCBI
4.4 years ago by K.Gee ▴ 40
0
votes
0
replies
702
views
Correlation test based on position sliding window for multiple variables
statistics R corr.test
4.4 years ago by User000 ▴ 750
0
votes
1
reply
967
views
Precision of variant calling (INDELs)
INDELs hap.py
updated 4.4 years ago by ▴ 290 • written 4.4 years ago by ▴ 30
0
votes
0
replies
845
views
How can I slicing to RS4 type in rpy2?
rpy2 slicing rs4 rpy
4.4 years ago by dxodnd • 0
0
votes
0
replies
983
views
Trycycler Assembly_Issue in Flye and MInimap2
Flye minimap2 Trycycler
4.4 years ago by Shiv_2 • 0
1
vote
1
reply
787
views
Combining results tables to plot automatecally
DESeq2
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 10
2
votes
2
replies
2.8k
views
scRNASeq equal number of cells across conditions
scRNAseq seurat
updated 4.4 years ago by 89k • written 4.4 years ago by ★ 4.8k
0
votes
0
replies
804
views
Job: HIRING: Postdoctoral Scholar in Genomic Epidemiology
postdoc epidemiology genomics
updated 4.2 years ago by 45k • written 4.4 years ago by ▴ 30
0
votes
0
replies
959
views
How to filter and impute missing snps in vcf file
Imputation SNPs PLINK VCF
4.4 years ago by Kumar ▴ 170
2
votes
2
replies
1.7k
views
Arlequin
phylogeny
updated 4.2 years ago by 45k • written 4.4 years ago by • 0
5
votes
6
replies
2.1k
views
How to verify putative miRNA
BLAST miRNA putative Automate
updated 4.0 years ago by ▴ 40 • written 4.4 years ago by ▴ 10
0
votes
0
replies
674
views
low unique mapped reads from STAR
sequencing rnaseq Alignment star
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
6
votes
3
replies
2.0k
views
comprehensive bacterial phylogenetic tree with edge lengths for all of RefSeq or Genbank at NCBI?
refseq ncbi tree phylogeny
4.4 years ago by cmo ▴ 90
2
votes
1
reply
1.0k
views
Checking for(a ton of) overrepresented sequences origins from 16S sequencing
Overrepresented Amplicon Blast FastQC Illumina
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 20
1
vote
2
replies
1.5k
views
multiqc report, should I care for "Per Base Sequence Content" module if using metagenomic datasets?
fastqc multiqc
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 140
0
votes
1
reply
818
views
RNA seq experiment design - two in house cell lines, data analysis with CCLE
RNAseq batch-effect experiment-design
updated 17 months ago by 45k • written 4.4 years ago by • 0
1
vote
4
replies
2.0k
views
Extract unmapped reads as pairs from (S/B)AM and create corresponding split read files.
bam sam unmapped paired fastq
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 40
6
votes
2
replies
1.7k
views
How to rename/replace the multiline fasta subsequence header in a fasta file?
DNA alignment fasta RNA
4.4 years ago by sunnykevin97 ▴ 1000
3
votes
5
replies
2.9k
views
Intall MAGIC-BLAST in Ubuntu from BASH SHELL in windows powershell.
magicblast ncbi ubuntu linux powershell
updated 5.0 years ago by 153k • written 5.0 years ago by • 0
0
votes
4
replies
2.0k
views
Mutect2 vcf.stats file missing
GATK mutect2 vcf.stats
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
1
vote
3
replies
2.2k
views
BWA mem or samtools have any parameter to filter the mismatch reads？
mapping samtools reads BWA
4.4 years ago by Damon_Wan • 0
4
votes
1
reply
1.5k
views
Uniprot Retrieve/ID mapping
Uniprot Mapping PDB2Uniprot
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 10
2
votes
7
replies
3.6k
views
CNVkit detected CNV number
CNVKit copynumbervariation cnr
updated 4.4 years ago by ★ 19k • written 4.4 years ago by ▴ 40
1
vote
2
replies
1.1k
views
igv track auto scaling fails in batch mode
igv
updated 4.4 years ago by 153k • written 4.6 years ago by • 0
0
votes
0
replies
1.1k
views
Error running MutSigCV: "missing mutation_type_dictionary_file"
error MutSigCV mutation type
4.4 years ago by alizee.diatchenko • 0
0
votes
0
replies
766
views
Negative homozygosity rates from plink --check-sex?
plink allosomes sex-check gwas
4.4 years ago by krassowski.michal ▴ 180
3
votes
7
replies
1.9k
views
How to download via biopython (proteom or genome) individual or random organisms?
genom proteom
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 30
8
votes
4
replies
3.4k
views
gzip: merged.fastq.gz not in gzip format
RNAseq
4.4 years ago by Kai_Qi ▴ 130
5
votes
1
reply
4.1k
views
1000 genomes project reference panel - GRCh38
GRCh38 build38 1KG reference_panel
updated 4.4 years ago by 2.9k • written 4.4 years ago by ▴ 130
1
vote
2
replies
1.8k
views
GATK no "SB" annotation after GenotypeGVCFs
gatk strandbias
4.4 years ago by wang.yiguan ▴ 10
0
votes
2
replies
1.1k
views
Converting tab character file to a tab delimited file
Linux
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 30
4
votes
6
replies
3.0k
views
Is number after "LOC" genes equal to its Entrez id ?
NCBI gene LOC
4.4 years ago by takoyaki ▴ 120
2
votes
3
replies
2.3k
views
Fragment length of paired-end data
paired-end
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 10
1
vote
0
replies
1.1k
views
Job: 2 PhD Scholarships in Bioinformatics in ancient sedimentary DNA and microbial DNA
metagenomics phd ancientdna sedadna ngs
4.4 years ago by Gabriel R. ★ 2.9k
1
vote
5
replies
1.9k
views
How to sort multi columns on long dataframe in R
data.frame Order R dplyr plyr
updated 4.4 years ago by ▴ 220 • written 4.4 years ago by ▴ 270
2
votes
20
replies
7.0k
views
Converting Braker2 gtf output to gff then genbank
annotation
4.4 years ago by robert.murphy ▴ 110
3
votes
1
reply
1.8k
views
Canu transcriptome assembly behavior
nanopore RNA-Seq canu
updated 4.4 years ago by ▴ 30 • written 4.7 years ago by ▴ 80
1
vote
1
reply
1.8k
views
Calculate P-value and FDR-adjusted P-value on normalized data
RPPA P-value FDR
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 10
2
votes
5
replies
2.1k
views
How to solve multiple CDS features with same locus tag in EMBL format
annotation embl
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 110
0
votes
4
replies
1.7k
views
Separate colors in immunohistochemical staining
image python
4.4 years ago by salvatore.raieli2 ▴ 90
0
votes
4
replies
2.5k
views
remove variable sites from vcf that only differ from reference.
vcf
updated 4.4 years ago by ▴ 170 • written 4.4 years ago by ▴ 60
2
votes
1
reply
3.0k
views
How to make consensus sequence from aligned reads ?
sequence Transcriptome aligned consensus reads
4.4 years ago by Info.shi ▴ 30
0
votes
0
replies
746
views
error when imputing for mismatch legend file
impute2 haps shapeit legend
4.4 years ago by raalsuwaidi ▴ 110
0
votes
2
replies
3.7k
views
Error in FUN(left, right) : non-numeric argument to binary operator in RStudio
rstudio
updated 4.4 years ago by 89k • written 4.4 years ago by • 0
0
votes
0
replies
742
views
How do I quickly run through all possible merger outputs?
unix emboss merger
4.4 years ago by lzbenicmi • 0
3
votes
3
replies
4.2k
views
Deeptools, ComputeMatrix and plotProfile
plotprofile ComputeMatrix deeptools Average
updated 4.4 years ago by • 0 • written 4.4 years ago by ▴ 20
2
votes
1
reply
636
views
How to merge SRRs from 1 sample
analysis NGS
updated 4.4 years ago by 153k • written 4.4 years ago by • 0
1
vote
2
replies
2.2k
views
Where to install latest Affymetrix Power Tools?
affymetrix
updated 4.4 years ago by 153k • written 4.4 years ago by ▴ 60
2
votes
9
replies
25k
views
7 follow
HISAT error: Encountered internal HISAT2 exception (#1)
RNA-Seq
updated 4.4 years ago by • 0 • written 8.3 years ago by ★ 1.5k
0
votes
0
replies
844
views
STAR - stringtie procedure
rnaseq AS stringtie splicing STAR
4.4 years ago by Hojn ▴ 30
121,896 results • Page 672 of 2438
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Comment: How to debug faulty BBmap clumpify command?
Answer: Yeast reference-based genome assembly
Answer: Structural Variant identification on pangenome graphs
Multiple VCF file comparision
Comment: Different UMAP for batch correction in R and Pytho
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful?
allele frequency in VCF
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Recent Replies
Comment: How to debug faulty BBmap clumpify command? by marongiu.luigi ▴ 760
Thank you. I am now using the latest version of BBmap and it works. There must have been a file corruption somewhere.
Comment: Yeast reference-based genome assembly by colindaven 7.9k
You're right about contiguity with these exceptionally short ONT reads, but there is no harm in trying. It depends on the repeat content of…
Comment: Transfer harmony-integrated scRNA-seq data to scanpy by Madiha ▴ 10
Hi, I am not sure if you still remmeber the solution you followed that time. But I am stuck with similar problem. scVI is not working good …
Answer: Pipeline for downloading, aligning, and curating influenza A and B sequences for by GenoMax 153k
Have you looked at https://nextstrain.org/ and specifically https://github.com/nextstrain/seasonal-flu Software is available to do the ana…
Comment: Different UMAP for batch correction in R and Pytho by GenoMax 153k
Use this tutorial for how to upload images: https://www.biostars.org/p/309884/#346553 Only difference is instead of using an external imag…
Answer: GTEx sQTL v8 – annotation version used? by GenoMax 153k
If you click over to the `Reference` tab ( https://gtexportal.org/home/downloads/adult-gtex/reference ), it looks like they used GENCODE v.…
Comment: How to Identify Conserved 21-mers Across TE Insertions in Drosophila? by manikin_python9f ▴ 20
Since they are transposons, we don’t know the exact location of them. We know their sequence of insertions from repeatmasker in dm6 genome.…
Comment: Tool 'sra_source' does not exist. by Atefeh • 0
Thanks for your kindness.
Comment: TCGA -derived Large RangeSummarizeExperient file by Tom • 0
It works well. Thank you very much ! @atpoint
Answer: TCGA -derived Large RangeSummarizeExperient file by ATpoint 89k
For the end user these `DFrames` are just regular data.frames, so you can do `col_data[,c("barcode", "patient", "whatever")]` or just do `a…
Comment: magpurify errors by shevch2009 ▴ 20
I have checked with my eyes, and I didn't find it, I have only one contig that starts with k127_458 .... but the name is different - k127_4…
Comment: Yeast reference-based genome assembly by Michael 56k
So, you aren't sure about the exact species? Then you might want to be careful with reference-based assembly in general. I recommend the fo…
Comment: Structural Variant identification on pangenome graphs by Panos ★ 1.8k
That's a very comprehensive list! Thanks for sharing! `minigraph` better suits my needs because all I need is SVs for my genomes. As far a…
Comment: Yeast reference-based genome assembly by amy967107 • 0
I have ~2.01 Gb of ONT data and the target genome is ~20–23 Mb (90–100× coverage). My ONT read N50 is ~3.8 kb, so contiguity may be limited…
Comment: Yeast reference-based genome assembly by amy967107 • 0
This is a yeast strain (probably Rhodotorula spp.) and I'm trying to assemble the entire genome from nanopore reads using a reference-based…
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