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122,211 results • Page 697 of 2445
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Homer annotatePeaks.pl motif density histogram output only showing 0s for motif occurrences
ATAC-seq Homer next-gen ChIP-Seq motif
4.7 years ago by rintsen.sherpa • 0
0
votes
6
replies
9.2k
views
How to keep only Biallelic SNP in vcf
snp
updated 4.7 years ago by 166k • written 4.7 years ago by ▴ 10
0
votes
0
replies
1.0k
views
Color nexus tree automatically using associated data
nexus ape ggtree R python
4.7 years ago by fhsantanna ▴ 620
1
vote
2
replies
1.6k
views
Handling single-cell RNA-seq data with very few cells and possible conversion to bulk-like RNA-seq
RNA-Seq
updated 4.7 years ago by 90k • written 4.7 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Bioinformatics Curator Positions with Computercraft @ NCBI
sequencing
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 90
6
votes
5
replies
4.5k
views
How Do You Align Or Compare Two Networks Content-Wise?
network graphs comparison
updated 4.7 years ago by 20 • written 15.0 years ago by ▴ 990
0
votes
0
replies
1.2k
views
Job: Bioinformatics Data Wrangler with Computercraft @ NCBI
data-wrangler sequencing genome
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 90
0
votes
1
reply
639
views
Checking sequence similarity between 2 RNAseq samples
RNA-Seq genome alignment sequencing
4.7 years ago by Triple Nipple ▴ 10
3
votes
1
reply
3.4k
views
How to speed up computeMatrix of deeptools?
software error
updated 4.7 years ago by ▴ 300 • written 5.4 years ago by ▴ 30
0
votes
2
replies
826
views
Deseq2 with opposite (dominant negative) design
RNA-Seq deseq2 R
updated 4.7 years ago by 15k • written 4.7 years ago by ▴ 50
5
votes
5
replies
2.2k
views
NetNGlyc: input sequence names are not unique: What means?
gene sequence glycosilation site-predictor
updated 4.7 years ago by ★ 30k • written 4.7 years ago by • 0
1
vote
4
replies
5.2k
views
Interpration of ridgeplot in transcriptomic analysis
RNA-Seq
updated 22 months ago by 45k • written 4.7 years ago by ▴ 60
4
votes
3
replies
1.8k
views
bowtie2 --passthrough, what does it do???
bowtie2 bowtie
4.7 years ago by mcrepeau ▴ 20
4
votes
6
replies
4.6k
views
Tools for straightforward visualization of alternative splicing events?
RNA-Seq Splicing
written 4.7 years ago by ▴ 40
2
votes
5
replies
3.9k
views
download all metadata from SRA
SRA
4.2 years ago by grant.hovhannisyan ★ 2.6k
0
votes
2
replies
2.1k
views
differential binding analysis of cut-tag peak data
ChIP-Seq
updated 4.7 years ago by 13k • written 4.7 years ago by ▴ 30
1
vote
3
replies
1.2k
views
How to identify 2 genes that have highly identical sequence
gene genome blastn gene identification
4.7 years ago by Ak ▴ 60
2
votes
5
replies
1.6k
views
Gene name put in volcano plot with already have file.
EdgeR volcano
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 40
0
votes
2
replies
1.5k
views
refGene Python Api
python api
4.7 years ago by Bala Hatun • 0
0
votes
0
replies
894
views
How to create marker file for Gistic?
gene gistic
updated 4.7 years ago by 154k • written 4.7 years ago by • 0
2
votes
0
replies
2.3k
views
Confusion over SNP strand importance re genotyping (G>C)
taqman genotyping strand dna SNP
updated 4.7 years ago by 20 • written 9.2 years ago by ▴ 20
1
vote
5
replies
2.5k
views
Replicates do not cluster together
r proteomics
updated 4.7 years ago by ★ 90k • written 4.7 years ago by ▴ 40
0
votes
0
replies
989
views
Job: PhD scholarship in bioinformatics in Rostock (Baltic Coast), Germany
aging nutrition
updated 2.7 years ago by 45k • written 4.7 years ago by • 0
0
votes
0
replies
594
views
Should one keep softmasking when combining gff+fasta to gbk format?
annotation
4.7 years ago by robert.murphy ▴ 110
0
votes
0
replies
513
views
Gwas on Window
alignment
updated 4.7 years ago by 166k • written 4.7 years ago by • 0
0
votes
0
replies
823
views
help regarding loading text files in affy package for background correction
R affy textfiles
4.7 years ago by raavi21198 ▴ 20
0
votes
1
reply
672
views
why i don not have peak when use DiffBind
ChIP-Seq
4.7 years ago by 17318598206 ▴ 30
1
vote
1
reply
949
views
how to get the best alignment from the sam file
RNA-Seq alignment
4.7 years ago by minghuiguo448 • 0
4
votes
2
replies
2.1k
views
R with HPC
R
updated 4.7 years ago by 9.0k • written 4.7 years ago by ▴ 30
5
votes
3
replies
1.8k
views
How to download RNA files in the easiest way? (from NCBI's SRA)
RNA-Seq rna-seq next-gen sequencing genome
4.7 years ago by GoldenRetriever ▴ 40
0
votes
0
replies
1.3k
views
News: :: FINAL CALL :: Online Course - A Practical Introduction to NGS Data Analysis (April 28 - 30, 2021)
NGS DNA-Seq Workshop Mapping RNA-Seq
4.7 years ago by David Langenberger 11k
0
votes
0
replies
1.5k
views
Problems running strelka2
variant calling ngs strelka
4.7 years ago by arne.zibat • 0
0
votes
0
replies
1.0k
views
Pymol to visualize MSA conservation
alignment sequence msa
4.7 years ago by katamaneni.akhila • 0
1
vote
0
replies
632
views
The problems of make_html.pl when install the miRDeep2
RNA-Seq
updated 4.7 years ago by 35k • written 4.7 years ago by ▴ 20
0
votes
0
replies
693
views
Question about a paper called Reference flow: reducing reference bias using multiple population genomes
RNA-Seq sequence
4.7 years ago by minghuiguo448 • 0
0
votes
0
replies
1.3k
views
Should I calculate beta diversity with or without rarefaction?
diversity R
4.7 years ago by dpc ▴ 250
0
votes
1
reply
2.3k
views
Generate consensus from contig alignment to reference sequence
Assembly alignment
4.7 years ago by daewowo ▴ 80
3
votes
1
reply
1.4k
views
What should be the value of Sjdboverhang in STAR?
STAR index reference sjdbOverhang
4.7 years ago by DareDevil ★ 4.5k
16
votes
13
replies
17k
views
Bash scripting FastQC for multiple fastq files in multiple directories
RNA-Seq bash fastQC
updated 4.7 years ago by ★ 4.5k • written 7.1 years ago by ▴ 20
0
votes
0
replies
1.3k
views
How maftools oncoplot deal with Splice_Site mutation
maftools oncoplot SNV Splicing
4.7 years ago by lincaijin1994 ▴ 50
1
vote
3
replies
1.3k
views
The problems when i install the miRDeep2
RNA-Seq
4.7 years ago by 51203903042 ▴ 20
0
votes
5
replies
1.2k
views
The problems when i map to genome by mapper.pl in miRDeep2
RNA-Seq
4.7 years ago by 51203903042 ▴ 20
4
votes
7
replies
1.8k
views
not able to run Deseq 2
RNA-Seq alignment sequence assembly
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 10
2
votes
4
replies
1.5k
views
Gene annotations of mammalian genomes
Gene annotation mammalian genomes
4.7 years ago by arsala521 ▴ 60
0
votes
0
replies
1.4k
views
Deletions are missed from consensus sequence even when they are predominant. Is this common to vcf2fq of vcfutils?
vcf2fq consensus bcftools indel
4.7 years ago by malaya77 • 0
2
votes
0
replies
1.2k
views
Tool: New location tracking tool for SARS-CoV-2 variant surveillance
sars-cov-2 variant covid-19
updated 2.5 years ago by 45k • written 4.7 years ago by ▴ 100
3
votes
3
replies
4.9k
views
Playing With Mysql/Ensembl (I): Mapping 'Gene' To 'Xref'
ensembl mysql
updated 2.1 years ago by 45k • written 15.7 years ago by 166k
1
vote
2
replies
1.1k
views
Seeking for siRNA screeing data analysis
R siRNA gene Statistic
4.7 years ago by podderbiswajit4 • 0
8
votes
1
reply
2.0k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 2.7 years ago by 45k • written 4.7 years ago by ★ 90k
3
votes
5
replies
1.3k
views
conceptual question about paired end sequencing
sequencing illumina
updated 4.7 years ago by 45k • written 4.7 years ago by ▴ 420
122,211 results • Page 697 of 2445
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what cause poly-G from NextSeq
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A: what cause poly-G from NextSeq
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How to trim transcripts using information from NCBI contamination screen report
How to trim transcripts using information from NCBI contamination screen report
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Recent Replies
Comment: best practice for diploid variant calling by Matteo Ungaro ▴ 130
@kevin thanks I was experimenting with the following since I already pursued most of the approaches you mentioned and, in practice, they ar…
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!
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