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85 results • Page
2 of 2
Sort: Rank
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Votes
Replies
0
votes
0
replies
92
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
3 days ago by
David
• 0
0
votes
2
replies
202
views
How to update R on ubuntu
installation
update
R
apt-get
3 days ago by
Bosberg
▴ 50
0
votes
0
replies
101
views
LEfSe
LEfSe
3 days ago by
benkosta
• 0
0
votes
0
replies
88
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
3 days ago by
Sara
▴ 30
0
votes
2
replies
151
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
3 days ago by
Lluís R.
★ 1.2k
0
votes
0
replies
97
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
3 days ago by
atharvakarkare14
▴ 30
0
votes
2
replies
197
views
What should I consider as FASTA for dataset?
PDB
FASTA
3 days ago by
Nafi
• 0
0
votes
0
replies
87
views
Differential accessibility using DiffBinf
diffbind
3 days ago by
Shloka
• 0
0
votes
0
replies
93
views
vg call vs vg surject
vg
variation
graphs
updated 3 days ago by
GenoMax
142k • written 4 days ago by
aliraza3119
• 0
0
votes
1
reply
129
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 3 days ago by
GenoMax
142k • written 4 days ago by
Winter
• 0
0
votes
1
reply
205
views
Finding batch and outlayers
Pca
updated 3 days ago by
christopher medway
▴ 450 • written 4 days ago by
Tigran
• 0
2
votes
2
replies
193
views
PDB related issue
rcsb
pdb
updated 4 days ago by
noodle
▴ 580 • written 4 days ago by
Nafi
• 0
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 3 days ago by
Ram
43k • written 8 months ago by
Gio
• 0
0
votes
1
reply
166
views
Downloading full alignments from Pfam
pfam
updated 4 days ago by
GenoMax
142k • written 4 days ago by
bef1
• 0
0
votes
0
replies
120
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 3 days ago by
dariober
14k • written 4 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
296
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 4 days ago by
ATpoint
82k • written 5 days ago by
Francesco
▴ 10
0
votes
0
replies
137
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
5 days ago by
tnminh89
▴ 10
0
votes
0
replies
141
views
Filter low express genes in microarray data
microarray
5 days ago by
Chris
▴ 260
0
votes
0
replies
565
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
6 days ago by
biocellbio
• 0
0
votes
0
replies
204
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
6 days ago by
HarperReed
• 0
1
vote
0
replies
158
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
6 days ago by
KABILAN
▴ 70
0
votes
0
replies
176
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 6 days ago by
Ram
43k • written 6 days ago by
SineWave
• 0
0
votes
0
replies
172
views
RNA-seq: full length gene
RNA-seq
updated 6 days ago by
Ram
43k • written 6 days ago by
Nargis
• 0
0
votes
3
replies
301
views
Highest variable features in single cell data
single-cell
updated 6 days ago by
bk11
★ 2.4k • written 7 days ago by
Kazo
▴ 10
1
vote
3
replies
373
views
PCA plot
DESeq2
PCAplot
updated 4 days ago by
LauferVA
4.2k • written 8 days ago by
Aaliya
▴ 10
0
votes
5
replies
364
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 5 days ago by
Istvan Albert
100k • written 8 days ago by
sehriban.buyukkilic
▴ 10
1
vote
8
replies
442
views
Downsampling fastq file
downsample
fastq
2 days ago by
marco.barr
▴ 90
0
votes
10
replies
489
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 10 days ago by
Patadu94
• 0
1
vote
2
replies
235
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 13 hours ago by
Ram
43k • written 17 days ago by
eesiribloom
▴ 80
0
votes
3
replies
328
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 3 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
2
votes
5
replies
927
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 3 days ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
0
votes
1
reply
510
views
HOMER on AWS
HOMER
updated 2 hours ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
3 days ago by
anna
▴ 20
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 8 hours ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 3 days ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
85 results • Page
2 of 2
Recent Votes
A: Iterating through paired-end reads in samtools / pysam
Answer: Where Can I Download Some Bam Files?
Download SAM/BAM files from SRA takes ages!!!
Comment: Bedtools merge minimum overlap?
Convert sra to bam file error handling
Answer: Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
Interpreting TCGA .rsem.genes.results and .rsem.genes.normalized_results files.
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Recent Replies
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
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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…
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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…
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3.9k
Imputation takes what? A day or two of compute time? Just re-do it.
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Thanks. Really appreciate your help with this. This site is such a great resource. The methods aren't totally clear on how they're gettin…
Comment: How to access TCGA samples that were treated with a specific drug?
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GenoMax
142k
It is possible that these drugs may not have been directly used in TCGA. Authors could have looked for mutations known to be acted on by th…
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Are you thinking about a specific scenario? If so, can you provide more info? I think the basic answer is that, yes, your choice of group C…
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by
harold.smith.tarheel
★ 4.9k
Bedtools [intersect][1] allows you to specify the fraction of overlap between two BED (or BAM) files using the F/f/r flags. You could split…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Sorry, I should have been more specific. By "that list" I mean what's populated in the Therapeutic Agents tab when no filters are applied. …
Comment: Bedtools merge minimum overlap?
by
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★ 2.4k
Not sure if you wanting to do like this- cat your_input.bed chr1 100 200 region1 + chr1 180 300 regi…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
If you know what the boundaries of your construct look like then trim the left-end of the read using the tag on that end (`ktrim=l`). Then …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Not every read in your data is going to match a guide. That is also true for sure. Let me clarify what I mean. For every read you should…
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anovak
▴ 120
If your GFA has paths in it that are P lines with names that don't include a sample name, contig name, and separators, then those are what …
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by
GenoMax
142k
> if you look at a fastq file you should be able to tell for every read definitely, if it has a perfect match for a guide in it and what gu…
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