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176 results • Page
2 of 4
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1
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3
replies
253
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 1 day ago by
GenoMax
142k • written 2 days ago by
jeffrey.maurer.informatics
• 0
1
vote
1
reply
91
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 4 hours ago by
Ram
43k • written 11 hours ago by
marco.barr
▴ 90
1
vote
8
replies
439
views
Downsampling fastq file
downsample
fastq
2 days ago by
marco.barr
▴ 90
1
vote
1
reply
204
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 2 days ago by
Michael
54k • written 2 days ago by
Lissa Cruz Saavedra
• 0
1
vote
2
replies
212
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 2 days ago by
Ram
43k • written 2 days ago by
Ravita
• 0
1
vote
2
replies
26
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
4 minutes ago by
Maverick
▴ 10
1
vote
4
replies
375
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
3 days ago by
hagl
▴ 10
1
vote
3
replies
62
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated just now by
jared.andrews07
★ 16k • written 3 hours ago by
yvonneh
▴ 10
1
vote
12
replies
2.1k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated just now by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
1
vote
3
replies
294
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 4 days ago by
ATpoint
82k • written 4 days ago by
Francesco
▴ 10
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
1
vote
3
replies
252
views
DESeq2 processing problems
deseq2
R
updated 1 day ago by
ATpoint
82k • written 1 day ago by
jagdish7921
• 0
1
vote
3
replies
370
views
PCA plot
DESeq2
PCAplot
updated 4 days ago by
LauferVA
4.2k • written 7 days ago by
Aaliya
▴ 10
1
vote
2
replies
330
views
ScRNAseq-How to correctly choose cell type marker genes
cellAssign
cell-markers
4 days ago by
Francesco
▴ 10
1
vote
3
replies
379
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 4 days ago by
Mensur Dlakic
★ 27k • written 5 days ago by
O.rka
▴ 710
1
vote
3
replies
80
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
updated 10 minutes ago by
GenoMax
142k • written 3 hours ago by
Qroid
▴ 40
1
vote
2
replies
268
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
1 day ago by
Nafi
• 0
1
vote
2
replies
214
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
14 hours ago by
rianna.collins
• 0
1
vote
2
replies
142
views
Odd alignment question/finding
Alignment
updated 12 hours ago by
ATpoint
82k • written 18 hours ago by
poordumbsillyidiot
• 0
1
vote
0
replies
156
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
6 days ago by
KABILAN
▴ 70
1
vote
0
replies
182
views
News:
Landscape Genomics course in Switzerland
LFMM
Landscape-Genomics
Sambada
R
Local-Adaptation
9 hours ago by
carlopecoraro2
★ 2.5k
1
vote
4
replies
1.0k
views
Filtering qscore on dorado
dorado
filtering
QC
nanopore
Guppy
6 hours ago by
eesiribloom
▴ 80
1
vote
7
replies
479
views
gvcf joint calling
WES
GATK
VCF
gVCF
4 days ago by
zihanss
• 0
1
vote
7
replies
484
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 3 days ago by
bk11
★ 2.4k • written 7 days ago by
starswillfade
▴ 10
1
vote
1
reply
95
views
Super ehancers
enhancers
updated 5 hours ago by
jared.andrews07
★ 16k • written 10 hours ago by
Oburah
• 0
0
votes
0
replies
63
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
23 hours ago by
meck
• 0
0
votes
0
replies
89
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 22 hours ago by
Ram
43k • written 1 day ago by
Oscar
▴ 10
0
votes
6
replies
418
views
Post-imputation plot
michigan-imputation-server
quality-control
22 hours ago by
kl
▴ 10
0
votes
1
reply
161
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 19 hours ago by
GenoMax
142k • written 23 hours ago by
mgranada3
▴ 30
0
votes
1
reply
547
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 18 hours ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
0
votes
0
replies
56
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
16 hours ago by
James
▴ 10
0
votes
1
reply
232
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 15 hours ago by
Scooter
▴ 280 • written 7 days ago by
avocado123
• 0
0
votes
0
replies
55
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
14 hours ago by
Vijith
▴ 30
0
votes
0
replies
46
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
11 hours ago by
Rhiannon
• 0
0
votes
0
replies
47
views
Use of annotation of integrated Seurat object in single sample
Seurat
9 hours ago by
Bine
▴ 60
0
votes
1
reply
171
views
Subsetting and merging back Seurat Object brings different results
Seurat
7 hours ago by
Bine
▴ 60
0
votes
6
replies
330
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
updated 5 hours ago by
GenoMax
142k • written 22 days ago by
eesiribloom
▴ 80
0
votes
4
replies
125
views
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 5 hours ago by
jared.andrews07
★ 16k • written 5 hours ago by
JH
• 0
0
votes
4
replies
231
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
5 hours ago by
matteo.levorato
• 0
0
votes
0
replies
51
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 4 hours ago by
Ram
43k • written 10 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
73
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 4 hours ago by
Ram
43k • written 11 hours ago by
4r-rtg
• 0
0
votes
1
reply
746
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 4 hours ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
426
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 4 hours ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
0
replies
26
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
3 hours ago by
Hang
• 0
0
votes
2
replies
84
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
2 hours ago by
Chen
• 0
0
votes
1
reply
67
views
RNA-seq data for deep learning classification
rna-seq
updated 2 hours ago by
dsull
★ 5.9k • written 4 hours ago by
Yuju
• 0
0
votes
0
replies
26
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
2 hours ago by
sovrappensiero
▴ 90
0
votes
1
reply
90
views
How to perform single cell multimodal integration using Seurat for Geo datasets
multimodal-analysis
single-cell
updated 1 hour ago by
Ram
43k • written 13 hours ago by
nithya
• 0
0
votes
2
replies
39
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 hour ago by
dtnondorf
• 0
0
votes
1
reply
45
views
Provean help
variant
Provean
updated 1 hour ago by
Mensur Dlakic
★ 27k • written 4 hours ago by
Arun Sai Kumar
• 0
176 results • Page
2 of 4
Recent Votes
Comment: Converting CRAM to FastQ
Answer: Download eQTL data of one specific gene for all tissues from GTEx
A: Tools To Calculate Average Coverage For A Bam File?
A: read depth using samtools
How to download raw sequence data from GEO/SRA
Tools To Calculate Average Coverage For A Bam File?
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Recent Replies
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Thank you so much! Will look it up right away.
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as yo…
Comment: Converting CRAM to FastQ
by
GenoMax
142k
Use `samtools view ` for this conversion. See discussion in https://www.biostars.org/p/9592860/ Specifically @jkbonfield's comment here --…
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
No that was only from Breast cancer. You could try selecting all data and see if you are able to see all treatments in the set. No idea a…
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
I don't think every guide is supposed to show up in these experiments as far as I have seen. You will get some guides with 0 counts as you …
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
> Can you try lowering the k to k=9? Wouldn't that mess with the results since all my kmers are 20bp? > You don't have any duplicate sequ…
Comment: Provean help
by
Mensur Dlakic
★ 27k
> Else, I will happy to send over the data and kindly perform the analysis for me. This website is meant to provide advice, not service. I…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thank you! Naive question, but does that list include all treatments in TCGA? I.e. is there anything missing from there, or that's it? Als…
Comment: Base Quality Score Recalibration with different reference genome
by
dtnondorf
• 0
Interesting! Thank you for such a quick response!
Comment: GATK genomicsDBimport intervals for WGS
by
Sd
• 0
I also have similar question. I sliced the genomic bed file with 50kb windows and 1kb padding into ~700 bed files; each bed file contains 9…
Comment: Base Quality Score Recalibration with different reference genome
by
GenoMax
142k
See answer here: https://www.biostars.org/p/9494503/#9494619 Heng Li said: https://twitter.com/lh3lh3/status/1410375781340135424 <!-- th…
Comment: DiffBind: no peaks in DBA
by
yvonneh
▴ 10
Ok fixed!
Comment: Extract gRNA sequence using cutadapt
by
GenoMax
142k
Can you try lowering the `k` to `k=9`? You don't have any duplicate sequences in your library file? That may be one reason why bbduk is r…
Comment: Extract gRNA sequence using cutadapt
by
gernophil
▴ 80
This topic is almost 5 years old, but I am facing the same (or at least a very similar) issue. I have ngs files from a CRISPR screen that …
Answer: RNA-seq data for deep learning classification
by
dsull
★ 5.9k
Honestly speaking, if it's deep learning, it probably doesn't matter that much if you use something like TPMs (probably not raw counts, unl…
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