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122,217 results • Page 718 of 2445
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0
votes
7
replies
7.8k
views
Phasing vcf file with Beagle
vcf phasing beagle haplotype bash
updated 4.5 years ago by • 0 • written 4.8 years ago by • 0
1
vote
1
reply
983
views
Genomic Variant calling from RNA-Seq Data
RNA-Seq SNP Genomic Variant
updated 4.8 years ago by ★ 90k • written 4.8 years ago by ▴ 200
7
votes
18
replies
7.3k
views
problem in matching the names between file names and patients Id in TCGA
TCGA CNV problem in matching
updated 4.8 years ago by ▴ 30 • written 7.5 years ago by ▴ 530
0
votes
3
replies
1.0k
views
Estrogen hormonal signalling genes
RNA-Seq
4.8 years ago by glady ▴ 320
0
votes
0
replies
622
views
How to find fixed mutations between populations
fixed mutations
4.8 years ago by Yongjie Zhang ▴ 110
6
votes
13
replies
2.5k
views
Blast in parallel with edible outfmt
blast output
updated 4.8 years ago by 90k • written 4.8 years ago by ▴ 40
2
votes
8
replies
2.3k
views
HDF5-DIAG: Error in using dsk
GATB
updated 4.8 years ago by ▴ 120 • written 4.8 years ago by • 0
2
votes
4
replies
1.6k
views
Two Sample t-test with bootstrapping for gene expression matrix in R
RNA-Seq R
updated 4.8 years ago by ★ 1.1k • written 4.8 years ago by ▴ 10
1
vote
1
reply
1.1k
views
Does transcriptome assembly data contains introns?
Transcriptome RNA-Seq Stringtie Hisat2 Assembly
updated 4.8 years ago by 16k • written 4.8 years ago by ▴ 20
0
votes
0
replies
864
views
Tools for structural variant on exome
exome sequencing SV structural variant
4.8 years ago by quentin54520 ▴ 120
1
vote
1
reply
3.3k
views
Samtools Mpileup Doesn'T Show Deletion, When Deletion Between Paddings
samtools mpileup bam ngs
updated 4.8 years ago by • 0 • written 12.7 years ago by ▴ 10
8
votes
22
replies
16k
views
Creating reference Index using Bowtie2
genome alignment next-gen Assembly
updated 4.1 years ago by 45k • written 11.4 years ago by ▴ 180
2
votes
6
replies
1.7k
views
change the header of fasta sequence
fasta name
written 4.8 years ago by ▴ 40
0
votes
0
replies
597
views
Are there any databases for gene co-expression or gene clustering by spatial/cell-type patterns?
rna-seq gene
4.8 years ago by Yep ▴ 20
0
votes
0
replies
709
views
Probability of rare variants
variants statistics probability
4.8 years ago by Genomics ▴ 20
1
vote
0
replies
655
views
Multifactor analysis in DESeq2
RNA-Seq
4.8 years ago by a.basitkhan1990 ▴ 60
0
votes
2
replies
1.3k
views
Stacks 1.44 Error
RAD-Seq ddRAD Stacks
updated 4.8 years ago by 35k • written 4.8 years ago by • 0
5
votes
4
replies
6.6k
views
How to download multiple fasta files from NCBI in linux command line?
fasta linux command line NCBI
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 80
2
votes
18
replies
4.0k
views
Uploaded bam file into IGV but couldn't see anything
alignment
4.8 years ago by dreamfeathers08 ▴ 10
0
votes
2
replies
1.6k
views
bigWig tracks inconsistent with MACS2 callpeak
ChIP-Seq MACS2
4.8 years ago by lida ▴ 10
3
votes
6
replies
4.0k
views
Problem using PicardTools MarkDuplicates: SortingCollection: There is not enough memory per file for buffering. Reading will be unbuffered.
genome
updated 4.8 years ago by 9.8k • written 4.8 years ago by • 0
0
votes
0
replies
954
views
Can I use FLEXBAR to detect and remove barcodes out of my short reads without demultiplexing ?
short reads Illumina barcodes removal FLEXBAR
4.8 years ago by giulia.trauzzi ▴ 30
0
votes
1
reply
1.3k
views
Structural variations intersection
next-gen SNP
updated 4.8 years ago by 20 • written 4.9 years ago by • 0
1
vote
0
replies
2.9k
views
Merging subsets in Seurat after SCTransform
seurat subset sctransform merge DEGs
4.8 years ago by VolEr ▴ 40
0
votes
0
replies
778
views
Missing S:N501Y from Clade 20H/501Y.V2 identified by Nextclade
Nextclade
4.8 years ago by arash.iranzadeh1980 ▴ 30
3
votes
6
replies
3.6k
views
User-defined coverage in CollectHsMetrics [Picard]
next-gen picard coverage broadinstitute
updated 4.8 years ago by • 0 • written 8.4 years ago by ▴ 190
3
votes
14
replies
3.9k
views
Samtools depth to get the read depth
sequencing RNA-Seq
4.8 years ago by bandanaschapagain ▴ 40
4
votes
4
replies
7.4k
views
How to get real cell names from Seurat Object?
rna-seq
updated 4.8 years ago by ▴ 250 • written 4.8 years ago by ▴ 150
0
votes
0
replies
867
views
Is there a way to identify which MSTRGs (novel StringTie transcripts) are potential novel ncRNAs?
MSTRG RNAseq StringTIe ncRNA Novel Transcripts
4.8 years ago by Jen ▴ 100
7
votes
23
replies
9.5k
views
Batch download genome feature file by RefSeq
gbff ncbi refseq
4.8 years ago by ben83 ▴ 50
3
votes
3
replies
4.9k
views
How to download a list of all KEGG orthologs with respect to KEGG module (or pathway) in Python?
kegg database python
updated 3.3 years ago by • 0 • written 4.8 years ago by ▴ 750
3
votes
2
replies
1.9k
views
How to check for completeness of a mitochondrial or chloroplast genome?
genome-completeness organelles
updated 2.2 years ago by 45k • written 4.8 years ago by ▴ 180
0
votes
2
replies
2.0k
views
minimap2 alignment for maker
maker minimap2 annotation alignment
4.8 years ago by gilsorek12 ▴ 10
0
votes
0
replies
723
views
How can I analyze a VCF dataset without an annotated reference genome
RNA-Seq R genome gatk galaxy
4.8 years ago by julianneradford ▴ 20
2
votes
6
replies
5.0k
views
convert DNA FASTA file to RNA FASTA file
RNA-Seq ChIP-Seq sequence
updated 4.8 years ago by 13k • written 4.8 years ago by ▴ 140
0
votes
0
replies
631
views
Centrifuge (Classifier for metagenomic sequences)
software error
4.8 years ago by amanpruthi15 • 0
0
votes
3
replies
2.2k
views
How can I run "gene set enrichment" (not necessarily GSEA) with only one condition?
metagenomics gene set enrichment analysis GSEA
4.8 years ago by O.rka ▴ 750
0
votes
0
replies
685
views
smallRNA-seq alignment with bowtie1:what is the argument for handling multi-mapped reads?
alignment smallRNA-seq bowtie1 multi-mapped reads
updated 4.8 years ago by 154k • written 4.8 years ago by • 0
1
vote
1
reply
1.7k
views
tsv file genome coverage
tsv genome
updated 4.8 years ago by 20 • written 4.8 years ago by ▴ 50
0
votes
8
replies
2.0k
views
Finding suboptimal alignments
sequencing DNA alignment
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 10
13
votes
11
replies
6.5k
views
8 follow
Visualization of protein structure in R (Shiny)
R rshiny pdb protein structure visualization
updated 4.7 years ago by ▴ 90 • written 5.2 years ago by ▴ 40
0
votes
1
reply
2.4k
views
Convert .sqn file to .gbk
organelle
updated 2.2 years ago by 45k • written 4.8 years ago by ▴ 180
1
vote
3
replies
2.6k
views
PCA with PLINK and SmartPCA: same imput file but different results in my plot. Why?
PCA PLINK smartPCA EIGENSTRAT plot
4.8 years ago by francesca94.minnai • 0
3
votes
1
reply
1.8k
views
Tool for extracting copy number alterations from a .maf mutation file
cna maf
updated 4.8 years ago by ★ 90k • written 4.8 years ago by ▴ 90
1
vote
4
replies
1.8k
views
Change sample order in plotHeatmap?
deepTools plotHeatmap computeMatrix
updated 3.3 years ago by • 0 • written 4.8 years ago by • 0
3
votes
5
replies
3.3k
views
Clustering sequences with low identity
clustering sequences
updated 4.8 years ago by ★ 30k • written 4.8 years ago by ▴ 870
0
votes
1
reply
831
views
ICGC data download
ICGC local server
4.8 years ago by Zahra ▴ 110
0
votes
1
reply
841
views
how to make BBmerge produce same strand fastq file
BBmerge
4.8 years ago by shangguandong1996 ▴ 30
3
votes
5
replies
2.2k
views
Newbie CIGAR question
SNP alignment sequence
updated 4.8 years ago by 20 • written 9.1 years ago by • 0
1
vote
0
replies
1.4k
views
How to get RSIDs of indels from GWAS summary statistics
R gene snp
4.8 years ago by Fede_Santos95 ▴ 20
122,217 results • Page 718 of 2445
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Comment: circos plot for genomic features
Answer: How to perform GO enrichment in non-model organisms?
Comment: circos plot for genomic features
Answer: How excactly is the Q30 is calculated?
A: PCA in a RNA seq analysis
what cause poly-G from NextSeq
what cause poly-G from NextSeq
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Recent Replies
Comment: Issue while running Kenddata. by GenoMax 154k
Look inside the `*.log` files to see if you can get additional clues (and post them here, if you can't figure out things). Check for lines …
Comment: Question about QC and scrublet by Arup Ghosh 3.5k
You can run Scrublet before filtering cells with high gene counts and compare the doublet score vs `n_counts_genes`.
Answer: How to perform GO enrichment in non-model organisms? by lieven.sterck 16k
In first instance you will as you say need to assign GOterms to your genes. eggNOG-mapper is certainly a valid approach to do this indeed. …
Comment: circos plot for genomic features by Matteo Ungaro ▴ 140
@colindaven thanks a lot! `clinker` also seems to be a nice/effective tool to do so. It happens we stuble across a work where they used `Ci…
Comment: circos plot for genomic features by colindaven 8.1k
Why not use something like Jbrowse2 instead ? https://jbrowse.org/jb2/gallery/ You can load both haplotypes, use minimap2 to create a paf …
Comment: How excactly is the Q30 is calculated? by colindaven 8.1k
This is really a question for your instrument provider. Only MGI application specialists and their bioinformaticians can really answer this…
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 ▴ 140
@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…
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