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122,201 results • Page 607 of 2445
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Need some help with next steps after getting fGSEA results from Microarray data.
microarray differential expression analysis fGSEA
updated 4.3 years ago by ▴ 20 • written 5.2 years ago by ▴ 110
0
votes
0
replies
3.4k
views
Seurat object
seuratobject seurat
updated 4.3 years ago by 9.0k • written 4.3 years ago by ▴ 30
0
votes
1
reply
826
views
Does genes for different subunits of a protein have different KO IDs?
kegg
updated 4.3 years ago by 3.9k • written 4.3 years ago by ▴ 250
0
votes
4
replies
2.5k
views
how to speed up SNP calling using bcftools
bcftools
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 60
2
votes
10
replies
3.8k
views
Why do I still have missing values in my gene list, even after cooksCutoff and independentFiltering have been set to FALSE ?
DESEQ2 missing symbol gene values
4.3 years ago by Sukrit • 0
0
votes
1
reply
831
views
Gene ontology
bn
updated 4.3 years ago by ▴ 520 • written 4.3 years ago by • 0
2
votes
2
replies
2.3k
views
Would you use HMMSCAN or HMMSEARCH when the query is much larger than the database?
nr hmmsearch hmmer hmm hmmscan
4.3 years ago by O.rka ▴ 750
0
votes
1
reply
777
views
Reading miRNA expression
cross-mapped read_count miRNA_ID reads_per_million_miRNA_mapped
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by • 0
0
votes
2
replies
1.1k
views
expression trend during cancer progression
T-stage
4.3 years ago by Amir.Asgary ▴ 30
5
votes
4
replies
8.9k
views
plot-vcfstats
bcftools snp vcf stats
4.3 years ago by rheab1230 ▴ 150
0
votes
2
replies
1.3k
views
parse out an EMBL record from a (file)
python
updated 4.3 years ago by 21k • written 4.3 years ago by ▴ 20
1
vote
0
replies
961
views
Why does STRUCTURE v2.3.4 (command line) does not work?
STRUCTURE SNPs bash
4.3 years ago by giulia.trauzzi ▴ 30
1
vote
7
replies
3.7k
views
vcf file summary
vcf summary statistics SNP
updated 4.3 years ago by ▴ 530 • written 4.3 years ago by ▴ 150
2
votes
3
replies
2.8k
views
Velocyto for smart seq2 taking an excessively long time (and memory)?
velocyto slurm RNAvelocity smart-seq2
4.3 years ago by skjw1029 ▴ 80
3
votes
3
replies
1.6k
views
Is there an online server to get a great phylogenetic tree?
phylogenetic tree
updated 4.3 years ago by ★ 30k • written 4.3 years ago by ▴ 10
0
votes
2
replies
1.3k
views
BCFtools -R stopped working
BCFtools
4.3 years ago by julia.zollner ▴ 20
2
votes
3
replies
1.6k
views
VG Installation with Ubuntu
vg vgteam
4.3 years ago by jdrubin • 0
2
votes
0
replies
1.1k
views
eggNOG v5 annotation file
eggNOG Annotation
4.3 years ago by Mehmet ▴ 820
0
votes
2
replies
1.7k
views
Jellyfish histo produces a blank file
genome jellyfish
updated 2.7 years ago by 45k • written 5.8 years ago by • 0
1
vote
0
replies
843
views
Weighted random walk in R
Walk Ranwom R Graph
4.3 years ago by Filago ▴ 110
5
votes
6
replies
3.3k
views
How to replace multiple string columns to binary values (0 and 1) in a dataframe?
dataframe R
updated 4.3 years ago by 21k • written 4.3 years ago by • 0
0
votes
19
replies
4.3k
views
error related to vcfstats
numpy snp vcf vcfstats
4.3 years ago by rheab1230 ▴ 150
0
votes
0
replies
547
views
differential gene expression analysis with Downstream analysis
TCGABiolinks Bioconductor
4.3 years ago by Gisele • 0
0
votes
0
replies
676
views
Comparing expression of a gene from different datasets in cBioportal
cbioportal expression median
4.3 years ago by Lordegod • 0
1
vote
4
replies
1.8k
views
convert detailed alignment format to fasta
alignment
updated 2.4 years ago by 45k • written 4.3 years ago by ▴ 10
3
votes
4
replies
4.0k
views
PLINK ASSOC : Skipping --assoc/--model since less than two phenotypes are present.
ASSOC PLINK phenotypes
4.3 years ago by Michal Nevo ▴ 140
0
votes
0
replies
906
views
Job: Bioinformatics Specialist - Torii Lab @ University of Texas at Austin (Texas, US)
NGS plants R
updated 2.7 years ago by 45k • written 4.3 years ago by • 0
0
votes
0
replies
989
views
Job: Postdoctoral Associate - Kuriyan Lab @ University of California, Berkeley (California, US)
biophysics biochemistry
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
0
votes
0
replies
799
views
Intersecting phyloP bed and per-base bed files
format bedtools bed
4.3 years ago by gokberk ▴ 90
0
votes
1
reply
1.0k
views
Job: Computational Biologist - Versiti Blood Research Institute, Milwaukee, WI, USA
computational-biologist
updated 2.5 years ago by 45k • written 4.3 years ago by • 0
0
votes
0
replies
672
views
Reducing the background noise of gene expression data
expression alzheimer dataset noise gene
4.3 years ago by Aram • 0
0
votes
2
replies
1.5k
views
individual-level allele frequencies
allele frequencies clustering plink
updated 4.3 years ago by 11k • written 5.2 years ago by ▴ 220
3
votes
11
replies
3.8k
views
I am converting the fq.gz. files (which are the results of the mgi study) to bam files to view on igv.
mem samtools bwa
updated 4.3 years ago by ★ 1.3k • written 4.3 years ago by • 0
0
votes
4
replies
2.8k
views
Is it possible for a cell cluster to not have cells of a certain condition?
seurat
updated 2.7 years ago by 45k • written 4.3 years ago by • 0
1
vote
4
replies
3.9k
views
Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (84, 195)
ATAC-seq PICARD
4.3 years ago by bill • 0
0
votes
2
replies
1.0k
views
Mapping taxonomy ID to virus host
host viruses taxid
4.3 years ago by Jagoda • 0
0
votes
3
replies
1.6k
views
Variant annotation using VEP
Annotation Zygosity VEP
updated 4.1 years ago by ▴ 20 • written 4.3 years ago by ▴ 40
124
votes
13
replies
188k
views
13 follow
How Can I Convert Bam To Sam?
bam next-gen-sequencing sam
updated 2.2 years ago by 45k • written 15.4 years ago by 5.0k
0
votes
0
replies
933
views
Herald: The Biostar Herald for Tuesday, August 03, 2021
herald
4.3 years ago by Biostar 3.7k
0
votes
2
replies
1.2k
views
Finding Molecular function for more than 100 GO terms
Gene Ontology
updated 4.3 years ago by 27k • written 4.3 years ago by ▴ 20
0
votes
0
replies
582
views
Is there any index could evaluate the polymorphic genes with SNPs and Indels in population ？
population polymorphism
4.3 years ago by Damon_Wan • 0
6
votes
11
replies
4.2k
views
Python fast way to get ONLY MAIN metadata for GSE ? (not walking through thousands underlying GSM-samples : slow or even endless)
GEO GEOparse
updated 4.3 years ago by 154k • written 4.3 years ago by ▴ 220
0
votes
0
replies
733
views
Calculating RMSD
RMSD alignment align protein
4.3 years ago by antoniaa ▴ 30
0
votes
1
reply
1.8k
views
How to download all sequences of a whole genome shotgun sequencing (WGS) project
seqrecords wgs ncbi
updated 4.3 years ago by ▴ 390 • written 4.3 years ago by ▴ 20
1
vote
0
replies
871
views
Job: Manager of Bioinformatics at Mogrify
Manager Python NGS SingleCellSequencing
4.3 years ago by Mogrify Talent Acquisition ▴ 10
1
vote
3
replies
2.7k
views
RNA-seq doesn't match qPCR and western blot results
qPCR siRNA RNA-seq
updated 4.3 years ago by ▴ 390 • written 4.3 years ago by ▴ 10
0
votes
1
reply
911
views
Obtaining mapped reads after extracting unmapped reads .
Unmapped samtools BAM
4.3 years ago by shrivadeepak • 0
2
votes
3
replies
1.4k
views
Using psi-blast to obtain all members of the protein family
psi-blast blast
updated 4.3 years ago by 9.0k • written 4.3 years ago by ▴ 30
0
votes
0
replies
461
views
Is it possible to analyze only a subset of genes from different microarray datasets?
microarray
4.3 years ago by iltan1 • 0
0
votes
0
replies
659
views
infer the orientation of z score by using the harmonisation codes
Gwas MR
4.3 years ago by celia • 0
122,201 results • Page 607 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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