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18 results • Page
1 of 1
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0
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18
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Generating mpileup file using samtools
mpileup
samtools
updated 11 minutes ago by
Joe
21k • written 32 minutes ago by
Ruqaiya
• 0
0
votes
0
replies
41
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
2 hours ago by
Vijith
▴ 30
0
votes
0
replies
41
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
4 hours ago by
Jeyong
• 0
0
votes
0
replies
50
views
Empty table plot using plotGseaTable()
FGSEA
12 hours ago by
Chris
▴ 260
1
vote
2
replies
120
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
13 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 14 hours ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
108
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
14 hours ago by
dtnondorf
• 0
0
votes
1
reply
124
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 6 hours ago by
Chris Dean
▴ 390 • written 15 hours ago by
sovrappensiero
▴ 90
2
votes
6
replies
246
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
9 hours ago by
Qroid
▴ 40
0
votes
1
reply
95
views
Provean help
variant
Provean
updated 14 hours ago by
Mensur Dlakic
★ 27k • written 17 hours ago by
Arun Sai Kumar
• 0
0
votes
0
replies
70
views
Use of annotation of integrated Seurat object in single sample
Seurat
23 hours ago by
Bine
▴ 60
0
votes
1
reply
193
views
Subsetting and merging back Seurat Object brings different results
Seurat
20 hours ago by
Bine
▴ 60
1
vote
1
reply
115
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 17 hours ago by
Ram
43k • written 1 day ago by
marco.barr
▴ 90
0
votes
1
reply
111
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 15 hours ago by
Ram
43k • written 1 day ago by
nithya
• 0
1
vote
3
replies
164
views
Odd alignment question/finding
Alignment
updated just now by
barslmn
★ 2.1k • written 1 day ago by
poordumbsillyidiot
• 0
1
vote
2
replies
235
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 17 hours ago by
Ram
43k • written 17 days ago by
eesiribloom
▴ 80
0
votes
1
reply
526
views
HOMER on AWS
HOMER
updated 6 hours ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 12 hours ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
18 results • Page
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Recent Votes
Comment: How to Calulate Allele Frequency from a VCF File?
Answer: Introduce SNPs on FASTA
Answer: how to split multi-fasta file into single fasta file named by header
How to Calulate Allele Frequency from a VCF File?
Answer: allele frequency in VCF
Answer: Two references 1. genome 2. plasmid for bowtie2
A: Iterating through paired-end reads in samtools / pysam
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Recent Replies
Comment: Odd alignment question/finding
by
barslmn
★ 2.1k
Maybe it is caused by fastp. https://github.com/OpenGene/fastp/issues/506
Comment: Generating mpileup file using samtools
by
Joe
21k
It's been a long time since I did this sort of thing, but I have a vague recollection that the mpileup process was made simpler and/or roll…
Comment: Introduce SNPs on FASTA
by
Riccardo
▴ 10
Thank you very much for your answer!
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This is great also for multiline fastas
Comment: how to split multi-fasta file into single fasta file named by header
by
rsieber
▴ 10
This only works for the first line of sequences.
Answer: What purposes can TPM values be used for?
by
b.contreras.moreira
▴ 180
In case it helps: https://haroldpimentel.wordpress.com/2014/05/08/what-the-fpkm-a-review-rna-seq-expression-units
Comment: What analysis suitable to identify similarly expressed genes between two samples
by
alifafiq1
• 0
Thank you @AT point. I was planning to use DESeq2 and use the alternate hypothesis (lessAbs) too considering that is the only package that …
Comment: Does comparing two different groups to a common third group introduce bias in th
by
ATpoint
82k
Note that by basic algebra A vs C and B vs C is the same as A vs B, so you might rethink your analysis to answer your question in a much si…
Comment: RNAseq one control two conditions, shared and exclusive genes
by
Mohamed Abderrahmane
▴ 20
Yes, why not? If it works for you like that, bingo!
Answer: Does comparing two different groups to a common third group introduce bias in th
by
christopher medway
▴ 450
You are testing groups A and B to a common baseline (C) - I don't see that there is anything wrong with doing that. It is a fairly common a…
Comment: HOMER on AWS
by
clairechung112
• 0
Hi. I guess it is solved by now, but as I did not find the answer immediately online, here is the answer I posted on a relevant question: h…
Answer: homer not configured properly
by
clairechung112
• 0
A late reply, but I just solved exactly the same error upon a request in the team. Please see if it helps in case anyone meets the same err…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
Was the spike-in a commercial product, e.g., from Zymo? Can you provide more information about what cells or DNA was spiked into your samp…
Comment: Bedtools merge minimum overlap?
by
Alex Reynolds
35k
Note that, in place of `sort-bed - | uniq -`, you can pass the `--unique` option to `sort-bed`. The input is not strictly a BED6 file, but…
Comment: Post-imputation plot
by
LChart
3.9k
Imputation takes what? A day or two of compute time? Just re-do it.
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