Limit : all time
all time today this week this month this year
50 results • Page 1 of 1
Sort: Rank
Rank Views Votes Replies
Showing top results for tag: next-gen • reset
3
votes
5
replies
1.1k
views
Does Last aligner only outputs the mapped reads to a bam file ?
assembly alignment sequencing next-gen genome
updated 4 days ago by • 0 • written 3.0 years ago by ▴ 130
0
votes
1
reply
98
views
reference-guided denovo assembly
next-gen denovo stringTie Assembly genome assembl reference-guided
updated 15 days ago by 104k • written 16 days ago by ▴ 30
3
votes
3
replies
2.0k
views
How to connect htseq-count to DESeq2?
R RNA-Seq next-gen DEG Mapping
updated 16 days ago by • 0 • written 24 months ago by ▴ 80
0
votes
4
replies
1.4k
views
eQTL analysis method (or pipeline) using ONLY RNA-seq data of alzheimer's disease mouse model
rna-seq sequence next-gen snp
updated 18 days ago by • 0 • written 3.5 years ago by • 0
1
vote
6
replies
418
views
CNVkit: not export cnr file
next-gen software error
updated 18 days ago by • 0 • written 11 months ago by ▴ 10
0
votes
2
replies
1.1k
views
Removing alternate alleles from .vcf
next-gen
updated 27 days ago by • 0 • written 2.4 years ago by ▴ 10
1
vote
8
replies
470
views
Visualization of RNA-SEQ Analysis
RNA-Seq sequence visualization next-gen
updated 26 days ago by 6.5k • written 28 days ago by ▴ 10
2
votes
5
replies
3.9k
views
6 follow
Where can I find mouse Gene MatriX file format (GMT)?
gene RNA-Seq next-gen
updated 4 weeks ago by • 0 • written 3.5 years ago by ▴ 180
0
votes
4
replies
797
views
Job: Graduate student position in bioinformatics available at the University of Iowa
genome next-gen ChIP-Seq RNA-Seq SNP Job
updated 5 weeks ago by • 0 • written 7 months ago by • 0
0
votes
0
replies
78
views
HOMER annotatepeaks.pl
ChIP-Seq HOMER sequencing next-gen
5 weeks ago by jjp55 ▴ 20
8
votes
8
replies
5.2k
views
TMM - Normalized FPKM values for RNASeq data ?
RNA-Seq next-gen R
updated 5 weeks ago by ★ 2.8k • written 5.2 years ago by ▴ 160
0
votes
1
reply
90
views
samtools mpileup: error CRC32 failure
sequencing SNP genome next-gen gene
updated 6 weeks ago by 137k • written 6 weeks ago by • 0
4
votes
6
replies
703
views
Trim bam file reads to the same length
RNA-Seq genome sequencing next-gen
updated 6 weeks ago by ★ 6.0k • written 18 months ago by ▴ 30
0
votes
4
replies
197
views
deeptools 3.5 plotCorrelation
ChIP-Seq sequencing plotCorrelation next-gen deeptools
updated 7 weeks ago by 6.5k • written 7 weeks ago by ▴ 20
0
votes
2
replies
138
views
Identical KEGG pathways enriched by up- and down-regulated genes
Kegg sequencing RNA-Seq next-gen
8 weeks ago by ashwing.kofficial ▴ 10
0
votes
2
replies
3.1k
views
Convert annovar file to vcf file
next-gen Assembly
updated 8 weeks ago by • 0 • written 6.3 years ago by ▴ 50
6
votes
8
replies
4.4k
views
7 follow
Any methods available to do QC analysis of Pacbio raw data??
Assembly genome Pacbio next-gen sequencing
updated 8 weeks ago by ★ 1.3k • written 3.8 years ago by ▴ 110
2
votes
4
replies
3.6k
views
TRINITY tool installation help
next-gen Assembly software sequencing error
updated 9 weeks ago by 34k • written 5.7 years ago by ▴ 40
0
votes
3
replies
911
views
Where to get genetic map build 38 ?
genome next-gen
updated 11 weeks ago by • 0 • written 3.2 years ago by ▴ 310
48
votes
17
replies
31k
views
17 follow
How To Get Number Of Reads In Bam File Efficiently In Python?
python samtools next-gen sequencing
updated 11 weeks ago by • 0 • written 11.0 years ago by ▴ 810
1
vote
2
replies
782
views
help to download Repbase repeatmasker
next-gen assembly software error
updated 3 months ago by ▴ 10 • written 10 months ago by • 0
0
votes
2
replies
1.3k
views
How to get SNPs genotype matrix from vcf file for JoinMap analysis?
snp next-gen R
updated 3 months ago by 13k • written 3.1 years ago by • 0
1
vote
3
replies
748
views
How to deal with the error for "Per Sequence GC Content" in FastQC tool?
sequencing sequence genome fastqc next-gen
updated 3 months ago by 104k • written 15 months ago by ▴ 20
3
votes
1
reply
469
views
Calling TE sequences from VCF files
next-gen sniffles variant_calling
updated 3 months ago by ▴ 20 • written 20 months ago by ▴ 80
1
vote
2
replies
475
views
Why is mapper.pl from mirdeep2 producing an empty mapping file?
mirna ngs next-gen
updated 3 months ago by ▴ 10 • written 7 months ago by ▴ 260
3
votes
3
replies
571
views
Downsampling fastq reads
next-gen metagenomics
updated 3 months ago by ▴ 280 • written 5 months ago by • 0
1
vote
2
replies
154
views
Want to know whether this p-adj value is acceptable
RNA-Seq next-gen sequencing
updated 4 months ago by 52k • written 4 months ago by ▴ 10
0
votes
6
replies
418
views
IDT xGen Exome Research Panel v2 vs Twist Human exome core
next-gen genome sequence
updated 4 months ago by ★ 2.3k • written 4 months ago by • 0
0
votes
1
reply
189
views
Cheat Sheet for NGS data analysis
next-gen cheat-sheet guidebook pdf NGS
4 months ago by angsudas62 • 0
0
votes
0
replies
227
views
Looking to annotate concatenated VCF files on Galaxy for Hg19 reference genome. Need setup guidance.
genome next-gen sequencing sequence gene
updated 4 months ago by 20 • written 5 months ago by ▴ 20
0
votes
0
replies
214
views
Homer annotatePeaks.pl motif density histogram output only showing 0s for motif occurrences
ATAC-seq Homer next-gen ChIP-Seq motif
4 months ago by rintsen.sherpa • 0
3
votes
4
replies
327
views
Split VCF into separate VCFs by SNP count
vcf bcftools next-gen
4 months ago by timothy.delory ▴ 20
5
votes
3
replies
194
views
How to download RNA files in the easiest way? (from NCBI's SRA)
RNA-Seq rna-seq next-gen sequencing genome
4 months ago by GoldenRetriever ▴ 40
3
votes
5
replies
284
views
PLINK:Error: Variant '.' is not biallelic. To obtain a full list of merge failures
SNP Assembly genome next-gen
4 months ago by williamsbrian5064 ▴ 390
0
votes
1
reply
150
views
How can I convert mouse microarray's Probe IDs into gene names?
R next-gen gene
4 months ago by moutazhatem.mh • 0
3
votes
3
replies
448
views
Help regarding RNAseq data analysis.
RNA-Seq alignment next-gen
updated 4 months ago by 20 • written 2.0 years ago by • 0
8
votes
10
replies
322
views
Performing Differential expression analysis using DESeq with 3 conditions
RNA-Seq Deseq2 R next-gen bioconductor
4 months ago by bionewbie • 0
5
votes
8
replies
304
views
A layman trying to understand what a FASTA file is
RNA-Seq sequencing next-gen gene tutorial
updated 4 months ago by 52k • written 4 months ago by ▴ 40
1
vote
2
replies
157
views
In-silico downsizing to estimate the DNA input
sequencing snp next-gen
updated 4 months ago by 9.8k • written 4 months ago by ▴ 30
0
votes
0
replies
153
views
Run TSS predator without TEX wig libraries
RNA-Seq sequencing next-gen software error
4 months ago by qstefano ▴ 20
0
votes
2
replies
217
views
How to perform Linkage Disequilibrium analysis for significantly associated K-mers?
next-gen genome snp assembly
updated 4 months ago by • 0 • written 4 months ago by ▴ 40
0
votes
0
replies
194
views
Is it possible to call variants using cram files?
next-gen sequencing SNP
4 months ago by vinayjrao ▴ 200
0
votes
2
replies
178
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 months ago by dk0319 ▴ 20
0
votes
1
reply
150
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 months ago by charleslindberg976 • 0
145
votes
34
replies
51k
views
31 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen tutorial Tutorial
updated 4 months ago by ▴ 120 • written 8.7 years ago by ★ 1.6k
1
vote
1
reply
284
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 months ago by 104k • written 4 months ago by • 0
0
votes
0
replies
247
views
Unable to convert from cram to bam
SNP software error sequencing next-gen
4 months ago by vinayjrao ▴ 200
0
votes
11
replies
273
views
Bowtie2: Mate file error & internal exception
alignment next-gen sequence
updated 4 months ago by 104k • written 4 months ago by • 0
0
votes
3
replies
542
views
How to get fastq files of SRA in Galaxy
RNA-Seq next-gen sequencing
updated 4 months ago by ▴ 40 • written 4 months ago by ▴ 10
1
vote
0
replies
297
views
Job: Postdoc Fellowships - EMBL | Stanford Life Science Alliance
rna-seq genome sequencing next-gen gene Job
4 months ago by stanford ▴ 10
50 results • Page 1 of 1
Recent Votes
Answer: Would this laptop be sufficient for small dataset/sequence analysis?
Answer: What's the biggest thing you dislike about bioinformatics?
Comment: opening downloaded files from STRING protein network without R
Comment: What's the biggest thing you dislike about bioinformatics?
Gene Set Enrichment Analysis
Comment: Removing genes of Seurat object during integration pipeline
How to generate a .sam/.bam file of a particular chromosome or even a particular region?
Recent Locations • All
Canada/University of Manitoba, 1 minute ago
United States, 1 minute ago
Sweden, 5 minutes ago
Boston, 5 minutes ago
United States, 5 minutes ago
USA, 6 minutes ago
Republic of Ireland, 7 minutes ago
Recent Awards • All
Teacher to WouterDeCoster 45k
Scholar to ATpoint 52k
Teacher to Kevin Blighe 75k
Scholar to Mensur Dlakic ★ 12k
Popular Question to irfanwustl ▴ 20
Teacher to Istvan Albert 88k
Popular Question to finswimmer 14k
Recent Replies
Answer: Would this laptop be sufficient for small dataset/sequence analysis? by Mensur Dlakic ★ 12k
16 GB of RAM will not cut it for any serious bioinformatics application these days. Doubly so if you choose to run Windows.
Comment: inquiry related to snpsift by Kevin Blighe 75k
I see - thanks. I am not sure that `SnpSift annotate` can do this, but you can first remove the original ID via `bcftools`, as follows: …
Answer: Forum: Job opportunities in Europe, with and without a PhD by Kevin Blighe 75k
South Africa? - very nice. I had been considering moving there, would you believe. There is no correct answer to your question, and one ca…
Comment: inquiry related to snpsift by rheab1230 • 0
the command: java -jar SnpSift.jar annotate dbSnp144.vcf variants.vcf > variants_annotated.vcf I am getting no error. the input file …
Comment: Displaying points which fall outside of the plot window in EnhancedVolcano by os306 ▴ 10
Hi there, just to follow up on this, I used your package to generate my volcano plots and got exactly what I was looking for. I now wish to…
Comment: inquiry related to snpsift by Kevin Blighe 75k
Hi, please show: 1. the command(s) that you are using 2. a sample of your input data 3. a sample of your output data 4. any status, wa…
Comment: opening downloaded files from STRING protein network without R by fionajcunningham • 0
thanks GenoMax I will try this sorry for delay in reply!! Fiona
Comment: What's the biggest thing you dislike about bioinformatics? by WouterDeCoster 45k
The alternative, constant off-by-one errors, aren't my idea of fun either :-)
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
Yeah, you can filter min_cells in Seurat with SCtransform. That would probably change the gene numbers in the SCT assay of the object. I u…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
Doesn't sctransform has a `min_cells` parameter that you could use here? It will only consider genes detected in at least `min_cells` cells…
Comment: Removing genes of Seurat object during integration pipeline by Stevens • 0
I was thinking of making it an arbitrary cut off of 10 cells, Seurat's documentation uses 3 for reading in a single sample. I believe that …
Answer: How To Split A Bam File By Chromosome by etiennedanis • 0
With samtools v1.11, ```samtools view -b in.bam chr1 > out.bam``` did not work for me. But ```samtools view -b in.bam 1 > out.bam``` wo…
Comment: Removing genes of Seurat object during integration pipeline by ATpoint 52k
What is a "few" cells? So how many? You would need to manually calculate the fraction of cells expressing a certain gene. Not sure in which…
Comment: I want to make a graph for conserved regions by sa.youssef • 0
Thanks so much, it is a great suggestion. may I ask you if you know a way to visualize the results of these data in my report? as we are wo…
Comment: Minfi - estimateCellCounts by Papyrus ★ 1.1k
I understand that you have whole blood samples and that's why you expect them to have more granulocytes? You could also try the [ENmix][1] …
Traffic: 1420 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6