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121,524 results • Page 425 of 2431
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519
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choose databbases in variant annotation
annotate Annovar
3.1 years ago by arwa.ahmad95 • 0
3
votes
3
replies
4.1k
views
Which pipeline to choose for RNA velocity
velocity 10x-genomics Seurat scRNA-seq
updated 2.9 years ago by ▴ 10 • written 3.2 years ago by ▴ 10
6
votes
6
replies
3.1k
views
agilent human all exon sureselct v7 bed file
exon human bed v7 agilent all sureselect
updated 14 months ago by ▴ 10 • written 3.1 years ago by • 0
4
votes
6
replies
1.5k
views
Difference between commands [bowtie2, samtools]
bowtie2 samtools
updated 3.1 years ago by 6.2k • written 3.1 years ago by ▴ 10
0
votes
3
replies
924
views
Mirdeep not giving results.
novel Mirdeep miRNA sequence RNA
updated 3.1 years ago by 56k • written 3.1 years ago by • 0
0
votes
1
reply
688
views
mkdir: cannot create directory ‘/home/neel@m95/Desktop/AMR/cgview_comparison_tool/cog_db’: Permission denied
CGView CCT
updated 3.1 years ago by 21k • written 3.1 years ago by ▴ 20
0
votes
2
replies
1.3k
views
Is it correct to use Tophat2 directly followed by Cuffquant to only align to the reference transcriptomes without wishing to assemble new transcripts?
Tophat2 Cuffquant Cufflinks
3.1 years ago by zoukai3412085 • 0
0
votes
2
replies
1.0k
views
minimum number of protein sequences for a sequence logo
logo
3.1 years ago by Stefano • 0
2
votes
1
reply
2.3k
views
How to choose threshold for filtering low counts before Voom transformation?
RNA-Seq R limma voom
updated 3.1 years ago by ★ 8.2k • written 4.9 years ago by ▴ 20
0
votes
2
replies
870
views
browser to visualize single cell data
scATAC-seq
updated 3.1 years ago by 15k • written 3.1 years ago by ★ 1.4k
1
vote
1
reply
1.2k
views
Handling NA values in limma's voom design matrix
rna-seq voom design.matrix limma NA
updated 3.1 years ago by 88k • written 3.2 years ago by ▴ 270
3
votes
6
replies
2.0k
views
Issue with trend line and confidence interval
geom_smooth ggplot
3.1 years ago by pdhrati02 ▴ 30
0
votes
1
reply
1.1k
views
WGCNA functions not found
wgcna
updated 3.1 years ago by ★ 1.6k • written 3.2 years ago by ▴ 30
2
votes
3
replies
1.8k
views
Determine sex/ gender of a mouse cell line via sequencing data
sequencing line cell
updated 3.0 years ago by ▴ 130 • written 3.2 years ago by ▴ 40
2
votes
5
replies
1.5k
views
ORFfinder length filter
Filter ORFfinder
updated 3.1 years ago by 56k • written 3.2 years ago by ▴ 60
2
votes
5
replies
1.6k
views
How to convert fastq to BAM
fastq bam
updated 3.2 years ago by ★ 4.2k • written 3.2 years ago by ▴ 30
0
votes
1
reply
720
views
RNAseq on dataset containing RPKM
expression differential
updated 3.2 years ago by 88k • written 3.2 years ago by ▴ 10
0
votes
0
replies
589
views
How to get list of blood-expressed Fantom 5 enhancers?
fantom5
updated 3.1 years ago by 45k • written 3.2 years ago by ▴ 270
2
votes
4
replies
2.6k
views
VCF Statistics
VCF satistics variants stats
updated 3.2 years ago by 166k • written 3.2 years ago by • 0
2
votes
11
replies
3.3k
views
plink bim file stops at chrM
plink chr bim
3.1 years ago by rturba ▴ 10
3
votes
1
reply
1.3k
views
How to run ROSE by a wet-lab research
ROSE
updated 3.2 years ago by 13k • written 3.3 years ago by • 0
0
votes
3
replies
1.4k
views
Connection refused FTPI NCBI NR DATABASE
NCBI refused Connection FTPI
updated 3.2 years ago by 152k • written 3.2 years ago by • 0
0
votes
5
replies
1.6k
views
different number of samples from each individual
statistics
updated 3.2 years ago by 89k • written 3.2 years ago by ▴ 150
7
votes
6
replies
2.7k
views
For loop in R
Kegg clusterprofiler R
updated 3.2 years ago by 21k • written 3.2 years ago by ▴ 80
1
vote
2
replies
1.1k
views
SnpEff filter PASS - what are the QC filters?
SnpEff
3.2 years ago by Jennifer • 0
0
votes
0
replies
655
views
error in getting mutation data
TCGA BRCA Mutation
updated 3.2 years ago by 45k • written 3.2 years ago by ▴ 30
0
votes
1
reply
1.2k
views
Transdecoder output for differential expression analyses: header problem
RNA-Seq Assembly software error genome alignment
updated 3.2 years ago by • 0 • written 4.6 years ago by ▴ 80
1
vote
1
reply
728
views
How to drop specific sites from VCFs?
vcf
updated 3.2 years ago by 152k • written 3.2 years ago by ▴ 70
1
vote
4
replies
2.8k
views
function GDCquery_Maf error
GDCquery_Maf R maftools
updated 3.2 years ago by ▴ 30 • written 3.2 years ago by • 0
7
votes
4
replies
1.4k
views
Trimming RNAseq data for transcriptome assembly
Rna-seq
updated 3.1 years ago by 45k • written 3.2 years ago by • 0
3
votes
4
replies
2.2k
views
STAR align quantMode
gene genecounts counts quantmode star
3.1 years ago by a_bis ▴ 40
0
votes
3
replies
1.1k
views
Statistical methods to determine descrimimant variables between two groups
multivariate R statistics Univariate
updated 3.2 years ago by 27k • written 3.2 years ago by ▴ 20
1
vote
1
reply
1.2k
views
Plink v1.9: Order of SNPs when extracting from file
plink
updated 3.2 years ago by 11k • written 3.2 years ago by • 0
2
votes
5
replies
1.5k
views
What does the sixth column of the unstranded bed file show +-?
bedtools RNA-seq bam star
updated 2.1 years ago by 45k • written 3.2 years ago by • 0
0
votes
2
replies
1.1k
views
Marking Duplicate reads in deep sequencing data
WES MarkDuplicates duplicates sequencing BAM
3.2 years ago by Tom • 0
4
votes
4
replies
1.5k
views
Split a fq file into two fq files by length.
split fastq
updated 3.2 years ago by 21k • written 3.2 years ago by • 0
0
votes
5
replies
1.9k
views
Genbank | large multi-isolate project
genbank ncbi
updated 3.2 years ago by ★ 3.8k • written 3.2 years ago by • 0
1
vote
2
replies
1.1k
views
Merge featurecounts lists
merge-lists featurecounts Rstudio dimension
3.2 years ago by imaparna27 ▴ 20
0
votes
0
replies
488
views
rows wise correlation between unequal columns
pandas correlation rows python datasets
3.2 years ago by pragatigga97 • 0
0
votes
0
replies
631
views
ION TORRENT data alignment
alignment torrent sequencing ion
3.2 years ago by deniselavezzari • 0
0
votes
1
reply
826
views
GSEA result interpretation
enrichment set Gene GSEA analysis
updated 3.2 years ago by 13k • written 3.2 years ago by ▴ 10
0
votes
0
replies
866
views
Using snpsift to annotate vcf with dbsnp and Clinvar
snpsift
3.2 years ago by whb ▴ 60
5
votes
4
replies
2.5k
views
gatk error: reference file does not exist
preprocessinterval linux gatk
3.1 years ago by parinv ▴ 80
0
votes
6
replies
1.7k
views
RNA sequencing
Genomics
3.2 years ago by aranyak111 • 0
3
votes
4
replies
1.7k
views
What is cut-off for significance in DE analysis in sc-RNA seq data
bulk expression differential single RNA-seq cell
updated 3.2 years ago by 88k • written 3.2 years ago by ▴ 10
36
votes
8
replies
12k
views
9 follow
Huge Tree Visualization
tree visualization
updated 3.1 years ago by ▴ 20 • written 15.1 years ago by ★ 1.5k
93
votes
19
replies
65k
views
18 follow
What Is A Good Phylogenetic Tree Display Program For Large Data Sets?
phylogenetics-tree
updated 2.1 years ago by 45k • written 14.8 years ago by ★ 2.6k
1
vote
1
reply
1.8k
views
DiffBind - Comparing normalization/background methods - how to create a heatmap (as in 7.5)?
DiffBind normalization ChIPseq
updated 3.2 years ago by ★ 2.1k • written 3.2 years ago by ▴ 20
0
votes
2
replies
4.2k
views
Issues removing unwanted taxa from phyloseq object
ASV phyloseq taxonomy dada2
updated 24 months ago by • 0 • written 3.3 years ago by • 0
0
votes
1
reply
1.2k
views
DiffBind using static set of peaks for all samples
DiffBind binding differential ChIP-seq peakset
updated 3.2 years ago by ★ 2.1k • written 3.2 years ago by • 0
121,524 results • Page 425 of 2431
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Answer: NCBI Datasets CLI Question
Answer: NCBI Datasets CLI Question
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss
Answer: NCBI Datasets CLI Question
SNP calling with SAMtools on multiple samples
Comment: Crac: Funny And/Or Weird Names For Bioinformatics Tools
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Answer: Which Reference Hg38 or T2T?? Both?? by GenoMax 152k
> So if I have my human sample and remove reads matching T2T, that Should? give me a host free set of reads??? For purpose of host deconta…
Comment: NCBI Datasets CLI Question by Bjorn • 0
Thanks! Works great.
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss by louisflower1999 • 0
Hi GenoMax, Thanks so much for your suggestion! Those amplicons are around 4.4kb. And there should be at least 1kb from the left and 800 b…
Comment: NCBI Datasets CLI Question by GenoMax 152k
Wanted to make it a complete answer with an additional command. Moved now.
Comment: NCBI Datasets CLI Question by Mensur Dlakic ★ 29k
Maybe make this an answer rather than a comment?
Comment: PCA interpretation by swbarnes2 15k
You are trying to PCA these by what, exactly? Binned coverage? Is this really informative?
Answer: NCBI Datasets CLI Question by GenoMax 152k
I don't see a way to specify a random number of accessions to download as an option. Perhaps you may want to open an issue and suggest that…
Comment: PacBio amplicon reads partially aligned using minimap2 – library or analysis iss by Zev.Kronenberg 12k
@genomax has a good point about trying `pbaa`. The tool will output consensus sequences of the different alleles. You can then use MSA to a…
Answer: Joint Calling for Large Germline WGS Cohort by Jeremy Leipzig 23k
Not to get too pedantic but joint genotyping solves a different problem (removing artefactual variants) from producing a population VCF tha…
Answer: Joint Calling for Large Germline WGS Cohort by DBScan ▴ 490
Another option would be HAILs VDS Combiner, [https://hail.is/docs/0.2/vds/hail.vds.combiner.VariantDatasetCombiner.html#hail.vds.combiner.V…
Comment: how shoud the phred score be intepreted? by QX ▴ 70
thank you for explanation and documentation
Comment: how shoud the phred score be intepreted? by GenoMax 152k
Illumina sequencing assumes/generally expects that clusters in a sequencing field have an even distribution of ACTG so for every sequencing…
Comment: how shoud the phred score be intepreted? by QX ▴ 70
what do you mean by 'low nucleotide diversity'. If it is low nucleotide diversity, is it supposed to have consistent signals, leading to hi…
Answer: how shoud the phred score be intepreted? by GenoMax 152k
> Does the phred-score is affected by the position of the base in all the reads (vertical), or all the bases that belong to a single read (…
Answer: Joint Calling for Large Germline WGS Cohort by Pierre Lindenbaum 166k
try glnexus https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started
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