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Altering bioawk script to take list.txt file as a command line parameter
bash shell-script
updated 3.0 years ago by 45k • written 4.7 years ago by ▴ 70
2
votes
1
reply
1.2k
views
Orthology and sequence identity/similarity
identity similarity orthology homology
updated 4.7 years ago by ★ 30k • written 4.7 years ago by ★ 2.9k
6
votes
0
replies
3.5k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
4.7 years ago by rpolicastro 13k
2
votes
3
replies
1.6k
views
DNA sequence simulator with different mutations rate per region
dna simulation mutation
updated 4.7 years ago by 103k • written 4.7 years ago by ★ 2.9k
1
vote
4
replies
11k
views
understanding the output files of fasterq-dump --split-files
fasterq-dump
updated 4.7 years ago by 45k • written 7.3 years ago by • 0
3
votes
4
replies
2.3k
views
How do we handle TPM values after converting from Ensembl to HUGO genes?
ensembl hugo tpm-calculator tpm rna-seq
updated 4.7 years ago by 103k • written 4.7 years ago by ★ 1.3k
4
votes
7
replies
4.3k
views
How to use Bowtie to align a list of fasta sequence to a reference genome?
mapping genome alignment fasta genomics
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 270
5
votes
3
replies
2.1k
views
What Machine Learning, AI, Deep Learning, & Neural Network Python packages do you use in Bioinformatics and/or whole genome sequencing annotation?
data python sequencing
updated 4.7 years ago by ★ 19k • written 4.7 years ago by ▴ 20
1
vote
0
replies
896
views
Empty result obtained when using SAMTOOLS and MPILEUP to generate consensus sequences FASTQ file
sequencing fasta fast dna
4.7 years ago by roelofco ▴ 10
1
vote
3
replies
9.8k
views
Update FAM file Plink for fid and pheno
FID fam plink phenotype
updated 4.7 years ago by 11k • written 4.7 years ago by • 0
0
votes
3
replies
1.4k
views
Could direction of reads affect the mapping of medium-size insertions
tmap INDELS
updated 4.7 years ago by 103k • written 4.7 years ago by • 0
1
vote
3
replies
3.3k
views
RSEM error: The adjacent two lines do not represent the two mates of a paired-end read!
rna alignment aligner
updated 4.7 years ago by 15k • written 4.7 years ago by ▴ 30
1
vote
0
replies
1.9k
views
Job: Computational Research Scientist: JG-Joint Genome Institute
general
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 70
0
votes
0
replies
1.7k
views
Job: Data Scientist: JG-Joint Genome Institute
genomics
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 70
0
votes
5
replies
2.2k
views
Issues with Centrifuge indexing
Centrifuge data
4.7 years ago by mcclurejenniferc • 0
2
votes
3
replies
2.8k
views
Explanation of Venn diagram output
general education
updated 4.7 years ago by 11k • written 4.7 years ago by ▴ 30
0
votes
0
replies
1.8k
views
Job: Computational Biology Program Developer
programming
4.7 years ago by BerkeleyLab ▴ 70
2
votes
3
replies
3.2k
views
Michigan imputation server quality control failed
imputation genotype
updated 4.7 years ago by 2.9k • written 6.7 years ago by ▴ 100
0
votes
0
replies
674
views
TWAS-hub interpretation: positive and negative values
hub twas
4.7 years ago by Friyunnwoo ▴ 20
6
votes
2
replies
2.7k
views
bcftools vcf2sex
genomics genome alignment genotyping
updated 4.7 years ago by ★ 1.5k • written 4.7 years ago by ▴ 540
2
votes
3
replies
2.8k
views
Alternatives to cytoscape for integrative analysis of Rna-seq data
rna-seq enrichment
updated 4.7 years ago by ▴ 130 • written 4.7 years ago by ▴ 10
4
votes
8
replies
9.3k
views
8 follow
Can not pass QC when doing imputation with Michigan Imputation Serve and Haplotype Reference Consortium panels
HRC 23andme imputation genotype
updated 3.3 years ago by 45k • written 9.8 years ago by ▴ 60
0
votes
0
replies
520
views
Database and webtools to analyze Barrett's esophagus
database genomics gene
4.7 years ago by Eko • 0
17
votes
14
replies
12k
views
11 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 17 months ago by 8.7k • written 4.7 years ago by ▴ 120
0
votes
0
replies
852
views
Visualisation of BGCs cluster on Antismash
antismash
4.7 years ago by Rima ▴ 20
0
votes
2
replies
1.9k
views
What is the best tools for circRNA analysis (extraction and quantification) ?
programming rna workflow
4.7 years ago by chloelaloe • 0
0
votes
0
replies
730
views
Taxonomic Bar Plots for too many values
taxonomy
updated 2.9 years ago by 45k • written 4.7 years ago by • 0
1
vote
2
replies
1.6k
views
Can I control the exposure time as a batch effect?
batch-effect RNA-seq time-series deseq2
updated 2.5 years ago by 45k • written 4.7 years ago by ▴ 190
2
votes
4
replies
2.0k
views
GTF format feature definitions
annotation
updated 4.7 years ago by 22k • written 4.7 years ago by ▴ 110
0
votes
4
replies
2.3k
views
Error in apply(counts, 2, function(x) rpkm(x, lengths)) : dim(X) must have a positive length
Rscript R
4.7 years ago by shail.nair05 ▴ 20
1
vote
1
reply
2.3k
views
What is the difference between breakends and breakpoints?
aligner genomics
updated 4.7 years ago by ▴ 290 • written 4.7 years ago by ▴ 30
4
votes
6
replies
1.9k
views
I want to reverse the fasta sequence
fasta
updated 4.7 years ago by 103k • written 4.7 years ago by ▴ 40
1
vote
3
replies
1.8k
views
Finding ORFs from RNA-seq Sequence Data of eukaryotic species
nucleotide rna dna genome
updated 4.7 years ago by ★ 2.9k • written 4.7 years ago by ▴ 10
0
votes
1
reply
1.1k
views
genotype matrix
structure python
updated 4.7 years ago by ▴ 290 • written 4.7 years ago by • 0
1
vote
0
replies
989
views
xpEHH
genomics test snp
4.7 years ago by dominik.lagler ▴ 30
4
votes
1
reply
1.4k
views
Are alternative splicing analysis and differential expression analysis of RNA-seq data both needed?
rna
updated 4.7 years ago by ▴ 300 • written 4.7 years ago by • 0
3
votes
3
replies
2.2k
views
GWAS Summary statistic
gwas
4.7 years ago by Kevin • 0
4
votes
6
replies
2.3k
views
best method for splicing variant analysis if I have the counts already?
Bioconductor RNA-seq splicinganalysis isoform
4.7 years ago by decppced • 0
1
vote
1
reply
2.9k
views
hypergeometric test for under-representation/over-representation of cells in a cluster (scRNA-seq) (in R)
rna test
updated 4.7 years ago by 13k • written 4.7 years ago by • 0
2
votes
4
replies
5.7k
views
i have proteomics data in .raw format
protein
updated 4.7 years ago by ▴ 940 • written 4.7 years ago by ▴ 30
0
votes
2
replies
1.2k
views
Concatenating fastq files for better assembly
genomics assembly sequencing RNA-Seq
4.7 years ago by shail.nair05 ▴ 20
0
votes
0
replies
735
views
copy number variation analysis
gisticfile copynumberalteration
4.7 years ago by Rob ▴ 180
0
votes
0
replies
639
views
Is there any way to fix this biplot so all the ids are able to be seen?
fasta R
4.7 years ago by trejomarco6 • 0
1
vote
1
reply
3.3k
views
Plink extract missing (and replaced) variant IDs from VCF
plink
updated 4.7 years ago by 11k • written 4.7 years ago by • 0
0
votes
1
reply
951
views
Question about the DbSNP reference vcfs
mapping dna
updated 4.7 years ago by ▴ 290 • written 4.7 years ago by ▴ 10
5
votes
2
replies
1.3k
views
Heirarchal regression for model comparison, RNA-seq
R RNA-seq heirarchalregression
updated 4.7 years ago by 90k • written 4.7 years ago by ▴ 300
3
votes
3
replies
2.3k
views
Create a seurat object from a DESeqDataSet
Seurat R DESeq2
updated 4.7 years ago by ★ 19k • written 4.7 years ago by ▴ 70
0
votes
0
replies
722
views
Motif analysis from the Binding and expression target analysis (BETA) software
workflow motif
4.7 years ago by mwong043 • 0
0
votes
0
replies
835
views
Gene enrichment analysis - How to get the gene names in Entrez id's?
Bioconductor Geneenrichment RNAseq genomics
updated 4.7 years ago by 166k • written 4.7 years ago by • 0
1
vote
4
replies
1.6k
views
Does 5' read trimming affect duplicate detection?
NGS
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 20
122,211 results • Page 694 of 2445
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what cause poly-G from NextSeq
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A: what cause poly-G from NextSeq
How to trim transcripts using information from NCBI contamination screen report
How to trim transcripts using information from NCBI contamination screen report
Trimming sequences based on NCBI contamination screen report
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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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