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116,725 results • Page
1 of 2335
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1
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11
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
updated 6 minutes ago by
GenoMax
142k • written 22 minutes ago by
Maverick
▴ 10
0
votes
0
replies
5
views
Bedtools merge minimum overlap?
bedtools
genomics
just now by
SJP
• 0
3
votes
8
replies
6.4k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 1 hour ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
36
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 hour ago by
dtnondorf
• 0
0
votes
0
replies
25
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
66
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
1
vote
3
replies
76
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
updated just now by
GenoMax
142k • written 3 hours ago by
Qroid
▴ 40
1
vote
2
replies
57
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
2 hours ago by
yvonneh
▴ 10
0
votes
0
replies
25
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
3 hours ago by
Hang
• 0
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
421
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
1
reply
44
views
Provean help
variant
Provean
updated 1 hour ago by
Mensur Dlakic
★ 27k • written 4 hours ago by
Arun Sai Kumar
• 0
1
vote
1
reply
87
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 4 hours ago by
bk11
★ 2.4k • written 14 hours ago by
Jeol
▴ 20
1
vote
1
reply
94
views
Super ehancers
enhancers
updated 5 hours ago by
jared.andrews07
★ 16k • written 10 hours ago by
Oburah
• 0
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
2
replies
81
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
2 hours ago by
Chen
• 0
5
votes
5
replies
173
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 5 hours ago by
atharvakarkare14
▴ 30 • written 9 hours ago by
Begonia_pavonina
▴ 150
0
votes
6
replies
329
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
1
vote
1
reply
94
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 4 hours ago by
Ram
43k • written 7 hours ago by
alifafiq1
• 0
0
votes
0
replies
46
views
Use of annotation of integrated Seurat object in single sample
Seurat
9 hours ago by
Bine
▴ 60
0
votes
0
replies
50
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
1
reply
169
views
Subsetting and merging back Seurat Object brings different results
Seurat
7 hours ago by
Bine
▴ 60
0
votes
0
replies
71
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 4 hours ago by
Ram
43k • written 10 hours ago by
4r-rtg
• 0
1
vote
1
reply
90
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 4 hours ago by
Ram
43k • written 11 hours ago by
marco.barr
▴ 90
0
votes
0
replies
45
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
11 hours ago by
Rhiannon
• 0
0
votes
1
reply
89
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
0
replies
54
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
14 hours ago by
Vijith
▴ 30
9
votes
10
replies
390
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 4 hours ago by
Zamin Iqbal
▴ 20 • written 1 day ago by
nicole.kavanagh
• 0
0
votes
1
reply
231
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
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
16 hours ago by
James
▴ 10
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
1
vote
2
replies
141
views
Odd alignment question/finding
Alignment
updated 12 hours ago by
ATpoint
82k • written 18 hours ago by
poordumbsillyidiot
• 0
0
votes
1
reply
160
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 19 hours ago by
GenoMax
142k • written 22 hours ago by
mgranada3
▴ 30
0
votes
0
replies
62
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
23 hours ago by
meck
• 0
0
votes
0
replies
88
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 22 hours ago by
Ram
43k • written 23 hours ago by
Oscar
▴ 10
0
votes
6
replies
416
views
Post-imputation plot
michigan-imputation-server
quality-control
21 hours ago by
kl
▴ 10
0
votes
1
reply
175
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 1 day ago by
Adam
▴ 30 • written 2 days ago by
J
• 0
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
0
votes
1
reply
745
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
108
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 1 day ago by
Ram
43k • written 1 day ago by
ernestine.kubi
• 0
0
votes
0
replies
76
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
1 day ago by
VITALA
• 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
0
votes
1
reply
149
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Edmond
• 0
0
votes
0
replies
115
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
1 day ago by
O.rka
▴ 710
0
votes
1
reply
419
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 1 day ago by
Ram
43k • written 1 day ago by
Dr Huma Naz
• 0
2
votes
2
replies
237
views
p-value in CIBERSORT
CIBERSORT
p-value
1 day ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
319
views
Telescope issue
Telescope
RNA-seq
updated 1 day ago by
GenoMax
142k • written 2 days ago by
eleven11
• 0
5
votes
6
replies
475
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 2 days ago by
me
▴ 760 • written 3 days ago by
Mariana
▴ 40
1
vote
1
reply
210
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 1 day ago by
Ram
43k • written 2 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
267
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
116,725 results • Page
1 of 2335
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Answer: Download eQTL data of one specific gene for all tissues from GTEx
A: Tools To Calculate Average Coverage For A Bam File?
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Recent Replies
Comment: How to access TCGA samples that were treated with a specific drug?
by
GenoMax
142k
No that was only from Breast. You could try selecting all data and see if you are able to see all treatments in the set. No idea about ho…
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…
Comment: How does gene length effect the number of reads mapped
by
Chen
• 0
Thanks for the detailed answer and I really appreciate it! I still have one question about why the number of reads can be influenced by the…
Comment: Split Fastq Files Into Chunks Of 1M Reads
by
thomas.heigl.ibk
• 0
i tried it. it splits, however, when i compare the first 8 lines of the second split file with the according lines from the original file, …
Comment: DiffBind: no peaks in DBA
by
Ram
43k
> I've also included the txt version of my .csv file No, you added a screenshot of plain text content, which is counterproductive. You can…
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