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326 results • Page
2 of 7
Sort: replies
Rank
Views
Votes
Replies
0
votes
4
replies
562
views
WGCNA Analysis - blockwiseModules data processing
WGCNA
blockwiseModules
updated 11 days ago by
GenoMax
136k • written 3 months ago by
Raito92
▴ 90
1
vote
4
replies
434
views
Indexing pubmed articles by data available?
search
data
pubmed
query
26 days ago by
LauferVA
3.8k
2
votes
4
replies
385
views
What are the steps for Germline and Somatic CNV detection using CNVkit?
cnv
cnvkit
10 days ago by
ahmad mousavi
▴ 760
1
vote
4
replies
266
views
Deseq2 5 level condition - building contrast
rna-seq
deseq2
updated 7 days ago by
ATpoint
78k • written 7 days ago by
annaA
▴ 10
1
vote
4
replies
407
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
12 days ago by
Daniel
▴ 30
0
votes
4
replies
234
views
Species coverage in the NCBI protein NR database ?
NR
updated 1 day ago by
Istvan Albert
99k • written 1 day ago by
HERMAN
▴ 10
0
votes
4
replies
320
views
very few sequences classified with Kraken2
metagenomics
16s
kraken2
kraken
updated 21 days ago by
dthorbur
▴ 860 • written 22 days ago by
10mz1
• 0
0
votes
4
replies
382
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
DiffBind
csaw
normalization
spikein
ChIPseq
11 days ago by
jared.andrews07
★ 16k
1
vote
4
replies
214
views
Bowtie mapping for single_end read
bowtie
12 hours ago by
Rita
• 0
0
votes
4
replies
302
views
rpy2 package
rpy2
25 days ago by
scarlettpigany
• 0
0
votes
4
replies
303
views
Query regarding callsets used as known sites in Variant Calling
GATK
VCF
9 days ago by
Shruti Baikerikar
• 0
0
votes
4
replies
416
views
scRNA-seq quality control
qc
scrnaseq
updated 14 days ago by
jv
★ 1.2k • written 18 days ago by
sarahmanderni
▴ 100
1
vote
4
replies
364
views
Efficient Bulk Data Retrieval from NCBI BioProject
ncbi
SRAtoolkit
prefetch
11 days ago by
George
• 0
1
vote
3
replies
133
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 4 hours ago by
dsull
★ 5.0k • written 7 hours ago by
RNAseqer
▴ 250
1
vote
3
replies
267
views
PMID multiple pdfs download using R
R
PubMed
updated 14 days ago by
Ram
41k • written 15 days ago by
Confused_human
▴ 10
1
vote
3
replies
299
views
gnomAD4.0 Hail Table Downloading
NGS
gnomAD
updated 11 days ago by
Ram
41k • written 11 days ago by
adarsh_pp
▴ 30
1
vote
3
replies
265
views
DNA/RNA Sequence Alignment
dna
rna
alignment
sequence
updated 13 days ago by
Mensur Dlakic
★ 25k • written 13 days ago by
Mirza
• 0
1
vote
3
replies
2.2k
views
BBMap : NH:i:1 and XT:A:R
bbmap
updated 6 days ago by
ayaosama2111
▴ 10 • written 7.0 years ago by
Nicolas Rosewick
10k
0
votes
3
replies
320
views
unbiased clustering of these top 50 genes in seurat
seurat
heatmap
updated 27 days ago by
Ram
41k • written 5 weeks ago by
odi
▴ 10
0
votes
3
replies
311
views
Correct for different number of cells and individuals in single cell data analysis
scRNA-seq
updated 25 days ago by
Ram
41k • written 25 days ago by
Sara
▴ 230
1
vote
3
replies
351
views
Differential Gene Expression between patients and not groups
differential-gene-expression
voom
limma
updated 22 days ago by
rpolicastro
12k • written 23 days ago by
Manuel
▴ 10
0
votes
3
replies
264
views
Jellyfish problem with Failed to open input file 'reads.jf'
jellyfish
kmer
fastq
7 days ago by
m.t.lorenc
• 0
0
votes
3
replies
329
views
STAR GeneCounts for most genes are 0
STAR
RNA-seq
updated 15 days ago by
Ram
41k • written 16 days ago by
Hansel Ivander
• 0
0
votes
3
replies
353
views
Two days_to_last_followups encountered when conducting Survival Analysis with TCGA Clinical Data
TCGA
Clinical
updated 10 days ago by
Zhenyu Zhang
★ 1.1k • written 23 days ago by
yukinoyou
• 0
0
votes
3
replies
399
views
vg call problem request
DEL
accuracy
INS
call
vg
updated 28 days ago by
dthorbur
▴ 860 • written 5 weeks ago by
20110700081
• 0
0
votes
3
replies
308
views
Package version warning - package ‘extdata’ is not available for Bioconductor version '3.17'
R
Bioconductor
updated 22 days ago by
Ram
41k • written 23 days ago by
Rob
▴ 160
0
votes
3
replies
81
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
updated 1 hour ago by
GenoMax
136k • written 3 hours ago by
cee28
• 0
4
votes
3
replies
326
views
Parsing columns with awk
awk
updated 29 days ago by
Ram
41k • written 29 days ago by
pablo
▴ 300
1
vote
3
replies
196
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 11 hours ago by
Nitin Narwade
★ 1.5k • written 18 hours ago by
Bine
▴ 50
0
votes
3
replies
285
views
overrepresented sequences in fastqc
fastqc
updated 25 days ago by
Ram
41k • written 25 days ago by
lonekaisar72
• 0
5
votes
3
replies
321
views
Strand bias in supplementary alignments from Nanopore
minimap2
nanopore
strand
updated 21 days ago by
cmdcolin
★ 3.4k • written 21 days ago by
dariober
14k
0
votes
3
replies
288
views
filtering lowly expressed exons
dexseq
deseq2
updated 11 days ago by
ATpoint
78k • written 15 days ago by
wiscoyogi
▴ 40
0
votes
3
replies
266
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
4 days ago by
Sara
▴ 230
0
votes
3
replies
315
views
RNA star taking more than 24h to complete 2nd pass
rna-seq
star
updated 12 days ago by
Ram
41k • written 12 days ago by
manuelmourato25
• 0
1
vote
3
replies
290
views
How to find transcription factor in my gene set
transcription-factor
updated 26 days ago by
Ram
41k • written 26 days ago by
Ishak
• 0
1
vote
3
replies
502
views
How to make the data compatible for DESeq2?
StringTie
counts
DESeq2
updated 27 days ago by
Ram
41k • written 15 months ago by
Karma
▴ 310
0
votes
3
replies
1.0k
views
Error with Ice normalization when running HiC-Pro
Hi-C
HiChIP
HiC-Pro
updated 2 days ago by
Cibo
• 0 • written 2.0 years ago by
Amina
• 0
2
votes
3
replies
305
views
Selecting a subset of MSigDB database for GSEA
fgsea
clusterprofiler
GSEA
12 days ago by
Orange
▴ 10
0
votes
3
replies
305
views
Reproducible seurat clustering
seurat
clustering
single-cell
updated 27 days ago by
Ram
41k • written 27 days ago by
synat.keam
▴ 80
0
votes
3
replies
307
views
Indexing the reference genome
STAR
updated 20 days ago by
Ram
41k • written 21 days ago by
Yasemin
• 0
1
vote
3
replies
264
views
Should unique gene names/transcript IDs be used for ribosomal gene copies in a GTF/GFF file?
GTF
GFF
updated 12 days ago by
dthorbur
▴ 860 • written 14 days ago by
cyril-cros
▴ 940
0
votes
3
replies
877
views
pal2nal -nogap -nomismatch options not working
pal2nal
updated 21 days ago by
wangjb702
• 0 • written 12 months ago by
pkfsantos
• 0
0
votes
3
replies
384
views
percentage of cells in each cluster- Seurat
seurat
updated 8 days ago by
seidel
11k • written 11 days ago by
odi
▴ 10
0
votes
3
replies
210
views
merged rs number information
merged
dbsnp
1 day ago by
sskimvd
• 0
3
votes
3
replies
283
views
How to proceed after Kraken2 analysis
rnaseq
kraken
updated 20 days ago by
dthorbur
▴ 860 • written 20 days ago by
pixie@bioinfo
★ 1.5k
0
votes
3
replies
368
views
Bowtie2 Error: reads file does not look like a FASTQ file
bowtie2
alignment
updated 18 days ago by
ATpoint
78k • written 11 weeks ago by
SO_Bio
• 0
0
votes
3
replies
330
views
Doheatmap in seurat
seurat
Heatmaps
updated 27 days ago by
Ram
41k • written 29 days ago by
odi
▴ 10
0
votes
3
replies
322
views
ANNOVAR Error: All variants in a VCF register as "invalid genotype records in input file"
genomics
wgs
vcf
annovar
updated 7 days ago by
MatthewP
★ 1.3k • written 8 days ago by
skinny_genes
• 0
0
votes
3
replies
295
views
Annovar - Annotated file cells show string
annovar
4 days ago by
Roshan
• 0
0
votes
3
replies
297
views
Appropriate genome reference for converting TCGA VCF files to MAF
maf
vcf
vcf2maf
TCGA
updated 10 days ago by
Zhenyu Zhang
★ 1.1k • written 14 days ago by
melissachua90
▴ 50
326 results • Page
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Answer: How should I run ssgsea analysis ?
Comment: Parsing XML file from dbGaP
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
Comment: SPAdes error: finished abnormally, OS return value: 21
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
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Comment: unicycler error : [Errno 13] Permission denied:
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Comment: Help doing differential expression analysis -experimental design and gProfiler T
by
rajabolacuan
• 0
Good Information Sir
Answer: Viral genes not showing up in combined mouse+virus alignment
by
cook.675
▴ 200
Hello I was curious to follow up and wonder if anyone knew why the viral genes are not showing up in the count matrix? I can't seem to solv…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴ 10
That makes sense. Thanks for the reminder.
Comment: bwa mem hangs after a few thousand reads
by
GenoMax
136k
Then you probably are best served by talking with your local sys admins to see where the issue may be.
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GenoMax
136k
> even if tpe and tbo are trailing after adapter and quality trimming Priority/order of operations in coded in the program. Brian will be …
Comment: bwa mem hangs after a few thousand reads
by
cee28
• 0
Actually, I originally did both of those things that you suggested. My original command at the top of the post was submitted to our cluster…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴ 10
The number of bases is still different even if `tpe` and `tbo` are trailing after adapter and quality trimming. So far for the RNA-seq proj…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GenoMax
136k
No there should not be much impact unless one of the reads has become substantially short compared to its mate. Strictly speaking you don't…
Comment: bwa mem hangs after a few thousand reads
by
GenoMax
136k
> I am running this on a HPC cluster. This is a guess but if you are actually running this on a cluster then it is possible that you need …
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴ 10
Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
DINESHR
• 0
Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint ![e…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres
by
dsull
★ 5.0k
Yeah, sometimes it looks "prettier" to plot p-value rather than adjusted p-value; although either one is technically ok to plot (even multi…
Comment: How to get unaligned reads and aligned reads into separate files from SAM/BAM?
by
rpolicastro
12k
I suppose if you really wanted to do it in one pass pysam would be an option. Courtesy of ChatGPT with a few modifications, and tested to s…
Comment: frequency plot for peaks
by
Ankit
▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
by
cmdcolin
★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
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