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122,212 results • Page 700 of 2445
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2
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2
replies
1.5k
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chr20_KI270871v1_alt in HG38 Broad Variant and Blacklist regions
ChIP-Seq
4.7 years ago by ahadli.farid ▴ 50
1
vote
6
replies
1.4k
views
Is it possible to get SARS-CoV-2 sequences from https://outbreak.info/?
sequence
4.7 years ago by Juke34 9.3k
0
votes
0
replies
1.0k
views
Difference between Go terms from blast hits and Interproscan in Blast2go
blast2go GO terms Interproscan Go graph
4.7 years ago by Kash ▴ 110
0
votes
0
replies
1.1k
views
Should i calculated Nm, UQ and MD tag of bam ?
alignment bam gatk
4.7 years ago by quentin54520 ▴ 120
11
votes
5
replies
11k
views
Remove supplementary alignments from a bam file
alignment
updated 4.7 years ago by • 0 • written 5.6 years ago by ▴ 90
3
votes
5
replies
1.8k
views
outlier detcection in a given gene expression datasets
R
updated 4.7 years ago by ▴ 270 • written 4.8 years ago by ▴ 70
0
votes
0
replies
699
views
Is there a curated list of non-genetic risk factors for diseases?
text mining risk factor
4.7 years ago by JorgeVallejo ▴ 20
0
votes
0
replies
751
views
Few samples for WGCNA coex network
RNA-Seq wgcna coexpression network
4.7 years ago by ovariohisterectomia ▴ 40
4
votes
3
replies
3.2k
views
featureCounts - Low Assigned rate - Locations of reads
RNA-Seq featureCount QC
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 80
3
votes
4
replies
2.7k
views
genes underlying gseGO categories
gseGO GSEA clusterProfiler enrichPlot
4.7 years ago by LacquerHed ▴ 30
2
votes
9
replies
2.6k
views
Setup PHG with Singularity
phg
updated 4.7 years ago by • 0 • written 4.8 years ago by ▴ 20
5
votes
4
replies
2.5k
views
hmmsearch output multiple alignment with initial query sequences
hmmer hmmsearch homology
updated 4.7 years ago by ★ 30k • written 4.7 years ago by ▴ 80
1
vote
5
replies
1.8k
views
Read count using htseq-count.
Assembly RNA-Seq gene
updated 2.7 years ago by 45k • written 4.7 years ago by ▴ 10
98
votes
12
replies
66k
views
6 follow
Ensembl-Ids Vs. Entrez-Ids
ensembl entrez gene
updated 4.7 years ago by ▴ 10 • written 13.9 years ago by ▴ 420
0
votes
3
replies
2.3k
views
readVCF in PopGenome can't open VCF file
RNA-Seq R vcf
4.7 years ago by julianneradford ▴ 20
2
votes
4
replies
2.5k
views
FeatureCounts output and downstream analysis
RNA-Seq sequencing featureCounts gene DESeq2
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 10
0
votes
0
replies
698
views
Mitigating technical allelic dropout in Single cell allelic RNA seq analysis
RNA-Seq rna-seq alignment sequencing sequence
4.7 years ago by luckysardar171 ▴ 20
0
votes
2
replies
907
views
How much sequencing coverage do you need in order to detect SNP's across the whole genome
sequencing SNP ChIP-Seq next-gen
4.7 years ago by dk0319 ▴ 70
1
vote
2
replies
905
views
How could I analyse the differential expression of a particular gene with RNA-seq data?
RNA-Seq gene
updated 4.7 years ago by 15k • written 4.7 years ago by • 0
1
vote
2
replies
1.5k
views
How to generate haplotypes with SNPs from WGS ?
SNP plink haplotype
updated 4.7 years ago by 11k • written 4.7 years ago by ▴ 10
1
vote
1
reply
1.1k
views
GO analysis: Why did gene set with high cluster frequency from up-regulation category will disappear from GO analysis of all DEGs ?
GO GSEA RNA-Seq sequencing
4.7 years ago by greyman ▴ 190
0
votes
1
reply
710
views
Is there a straightforward way to use RNA alignment with the genome to infer exon-intron structure?
RNA-Seq genome alignment sequencing next-gen
4.7 years ago by charleslindberg976 • 0
149
votes
35
replies
67k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 2.8 years ago by 45k • written 13.0 years ago by ★ 1.6k
0
votes
1
reply
786
views
delete several ranges from a DNA sequence
genome slicing delete segments
updated 4.7 years ago by 13k • written 4.7 years ago by • 0
4
votes
2
replies
1.7k
views
TSS predator input files
RNA-Seq software error alignment
updated 4.7 years ago by ★ 2.1k • written 4.7 years ago by ▴ 20
1
vote
3
replies
22k
views
bed to vcf format conversion
bed vcf
updated 2.7 years ago by 45k • written 9.5 years ago by ▴ 10
0
votes
5
replies
5.0k
views
DEGpatterns and functional analysis of clusters
RNA-Seq DEGreport DESeq2 R
updated 4.7 years ago by ★ 90k • written 4.7 years ago by • 0
2
votes
2
replies
1.6k
views
Diffbind-weird Fold value
ChIP-Seq
updated 4.7 years ago by ★ 2.2k • written 4.7 years ago by • 0
0
votes
0
replies
709
views
How can I download Methylation data for MethylMix package. (unusual error popped)
R software error MethylMix Methylation
4.7 years ago by shlokanegi.phe18 • 0
0
votes
0
replies
1.7k
views
Job: PhD student in precision cancer bioinformatics | Charite, Berlin, Germany
cancer berlin precision-cancer ngs
updated 2.3 years ago by 45k • written 4.7 years ago by • 0
1
vote
3
replies
1.4k
views
How do I perform MAF analysis for each family separately in PLINK?
plink family population split MAF
4.7 years ago by Alana.selli • 0
6
votes
10
replies
1.8k
views
Power of differential expression for a single gene analysis
RNA-Seq
4.7 years ago by German.M.Demidov ★ 3.0k
0
votes
0
replies
799
views
How to calculate expected heterozygosity(he) by MSA
gene software error miceosatellite MSA
updated 4.7 years ago by 20 • written 4.7 years ago by • 0
2
votes
3
replies
1.4k
views
RNASeq alignment visualisation
alignment RNA-Seq Assembly
4.7 years ago by daewowo ▴ 80
1
vote
1
reply
1.3k
views
Could adaptor contamination and primer dimers lead to low number of cells detected during a single cell RNA sequencing ?
RNA-Seq rna-seq alignment sequencing next-gen
updated 4.7 years ago by 154k • written 4.7 years ago by ▴ 10
0
votes
2
replies
1.5k
views
How to generate dotplot using the lastz output file
R alignment
updated 2.5 years ago by 45k • written 4.7 years ago by • 0
0
votes
0
replies
965
views
News: Introduction to Deep Learning
Machine-Learning Deep-Learning Python
updated 2.8 years ago by 45k • written 4.7 years ago by ★ 2.7k
0
votes
3
replies
1.8k
views
prefetch and fast-dump problems?
prefetch SRA fastq-dump
updated 2.7 years ago by 45k • written 4.8 years ago by ▴ 270
2
votes
5
replies
1.9k
views
Select and keep only some results from DESEq2
RNA-Seq DESEq2 results R
4.7 years ago by luzglongoria ▴ 50
0
votes
0
replies
1.2k
views
Error while using blastdb_aliastool - Some referenced files may be missing
blast localblast blastdb_aliastool
4.7 years ago by Sai • 0
0
votes
0
replies
444
views
Construct consensus from SE mRNA dataset
RNA-Seq Assembly
4.7 years ago by Emma • 0
17
votes
16
replies
25k
views
9 follow
Ensembl ID to ENTREZ best converter
gene
updated 12 months ago by 3.5k • written 5.5 years ago by ▴ 370
8
votes
8
replies
9.3k
views
Differential protein/biomarker expression using limma: is that possible?
RNA-Seq NPX LIMMA PROTEOMICS microarray
updated 4.5 years ago by ▴ 40 • written 4.7 years ago by ▴ 130
0
votes
3
replies
925
views
Not getting the same results with biopython and NCBI
biopython
4.7 years ago by Harper • 0
0
votes
0
replies
569
views
Are TSL flag reliable for lncRNA annotation?
genome gene
4.7 years ago by imli_lkr • 0
0
votes
1
reply
1.4k
views
Accessing tar File Data from cBioPortal
RNA-Seq
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 50
0
votes
1
reply
1.2k
views
Help me solve this error in bigSCale2
bigSCale2 scRNAseq
updated 4.7 years ago by 5.9k • written 4.7 years ago by • 0
0
votes
0
replies
1.2k
views
Unable to convert from cram to bam
SNP software error sequencing next-gen
4.7 years ago by vinayjrao ▴ 260
0
votes
0
replies
752
views
Strange gstacks warning
stacks gstacks
4.7 years ago by mcrepeau ▴ 20
0
votes
1
reply
1.0k
views
What is each sample?
scRNA-seq
4.7 years ago by pomodoro_sinensis ▴ 130
122,212 results • Page 700 of 2445
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Recent Replies
Answer: How excactly is the Q30 is calculated? by GenoMax 154k
[**Phred quality scores**][1] have been in use since the 1990s and early days of human genome project. They were co-opted in the fastq form…
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…
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