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336 results • Page
2 of 7
Sort: Views
Rank
Views
Votes
Replies
0
votes
1
reply
485
views
FASTQ files for 30x 1KGP of Phase 3 data
1000genomes
fastq
updated 2 days ago by
Ram
41k • written 13 months ago by
Qboy
• 0
2
votes
6
replies
475
views
Burrows-Wheeler transform
Python
BWT
DNA
updated 26 days ago by
Ram
41k • written 27 days ago by
Balqees
• 0
4
votes
6
replies
474
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
10 days ago by
cee28
▴ 30
0
votes
1
reply
469
views
Error in H5Fopen
atac-seq
scatac-seq
updated 24 days ago by
caiden.golder
• 0 • written 17 months ago by
bioinformatics.girl
▴ 20
0
votes
5
replies
465
views
bam file missing barcode and UMI info
barcode
star
starsolo
updated 29 days ago by
GenoMax
136k • written 4 weeks ago by
malonzm1
• 0
0
votes
1
reply
456
views
Loftee no splice site annotations
Loftee
VEP
updated 9 days ago by
AMARU
• 0 • written 21 months ago by
Filago
▴ 90
2
votes
3
replies
455
views
How to check if my sequence is DNA or Protein in BioPython?
genomics
biopython
fasta
updated 26 days ago by
Joe
21k • written 29 days ago by
O.rka
▴ 710
0
votes
4
replies
444
views
scRNA-seq quality control
qc
scrnaseq
updated 25 days ago by
jv
★ 1.3k • written 29 days ago by
sarahmanderni
▴ 100
0
votes
7
replies
440
views
Using Primer3 with python to genotype a SNP at a particular position
primer3
python
position
primer
updated 23 days ago by
Pierre Lindenbaum
158k • written 23 days ago by
Keith
• 0
3
votes
4
replies
438
views
Downstream analysis with DEseq2 normalization
DEseq2
integration
19 days ago by
QX
• 0
1
vote
4
replies
429
views
Converting IGV to Figure using Illustrator (or other tools)
Illustrator
IGV
23 days ago by
Daniel
▴ 30
0
votes
2
replies
427
views
Corrupted sam file from bwa. [W::sam_parse1] mapped query cannot have zero coordinate; treated as unmapped
samtools
bwa
updated 19 days ago by
jkbonfield
★ 1.2k • written 24 days ago by
tnminh89
▴ 10
0
votes
4
replies
413
views
Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions
DiffBind
csaw
normalization
spikein
ChIPseq
22 days ago by
jared.andrews07
★ 16k
4
votes
6
replies
412
views
Unexpected separation of RNA-seq samples on PCA plot
depletion
PCA
rRNA
plot
RNA-seq
19 days ago by
Tihana
▴ 10
0
votes
6
replies
411
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
10 days ago by
tw_140
• 0
0
votes
3
replies
411
views
percentage of cells in each cluster- Seurat
seurat
updated 19 days ago by
seidel
11k • written 22 days ago by
odi
▴ 10
2
votes
4
replies
410
views
What are the steps for Germline and Somatic CNV detection using CNVkit?
cnv
cnvkit
21 days ago by
ahmad mousavi
▴ 770
1
vote
6
replies
395
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
11 days ago by
CTLong
▴ 50
1
vote
5
replies
391
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
updated 2 days ago by
Rory Stark
★ 2.0k • written 11 days ago by
DINESHR
• 0
1
vote
4
replies
387
views
Efficient Bulk Data Retrieval from NCBI BioProject
ncbi
SRAtoolkit
prefetch
22 days ago by
George
• 0
0
votes
3
replies
385
views
Bowtie2 Error: reads file does not look like a FASTQ file
bowtie2
alignment
updated 29 days ago by
ATpoint
78k • written 3 months ago by
SO_Bio
• 0
0
votes
3
replies
379
views
Two days_to_last_followups encountered when conducting Survival Analysis with TCGA Clinical Data
TCGA
Clinical
updated 21 days ago by
Zhenyu Zhang
★ 1.1k • written 4 weeks ago by
yukinoyou
• 0
0
votes
3
replies
376
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 14 days ago by
ATpoint
78k • written 15 days ago by
manuelmourato25
• 0
2
votes
4
replies
367
views
An issue with gtf file (ballgownrsem)
Ballgown
RNA-seq
GTF
RSEM
3 days ago by
cucindarko51
• 0
1
vote
1
reply
366
views
Trinity 'genes' too much
Trinity
RNA-seq
updated 4 days ago by
Ram
41k • written 2.1 years ago by
Hou
• 0
0
votes
1
reply
363
views
How to use conumee segment mean for gistic input
genomics
gistic
NGS
methylation
conumee
updated 10 days ago by
sativus
▴ 10 • written 14 months ago by
Thind amarinder
▴ 340
0
votes
2
replies
360
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 9 days ago by
fracarb8
★ 1.3k • written 10 days ago by
synat.keam
▴ 80
0
votes
0
replies
356
views
CalcPerturbSig() Seurat
scRNA-seq
single-cell
differential-expression
Seurat
updated 19 days ago by
Ram
41k • written 9 months ago by
123
• 0
0
votes
3
replies
354
views
ANNOVAR Error: All variants in a VCF register as "invalid genotype records in input file"
genomics
wgs
vcf
annovar
updated 18 days ago by
MatthewP
★ 1.3k • written 19 days ago by
skinny_genes
• 0
1
vote
3
replies
348
views
Bam files generated with STAR cause a segmentation fault core dump error when used with another tool
RNA-Seq
mapping
updated 5 days ago by
GenoMax
136k • written 6 days ago by
bkffadia
• 0
0
votes
7
replies
346
views
SNP calling with many samples using bcftools
bcftools
SNP
multithreading
23 days ago by
George
• 0
1
vote
5
replies
345
views
bcftools mipileup error: format error, unexpected A at line 1
bcftools
updated 26 days ago by
Jautis
▴ 520 • written 26 days ago by
jiyoung
▴ 20
3
votes
4
replies
345
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 10 days ago by
Nitin Narwade
★ 1.5k • written 11 days ago by
RNAseqer
▴ 250
1
vote
9
replies
344
views
Htseq-count reads with missing mate encountered
htseq
htseq-count
24 days ago by
Bjorn
• 0
0
votes
2
replies
344
views
How to perform liftover from 38 to 37 in R?
R
genomics
hail
liftover
gwas
21 days ago by
DN99
▴ 20
0
votes
3
replies
343
views
STAR GeneCounts for most genes are 0
STAR
RNA-seq
updated 26 days ago by
Ram
41k • written 27 days ago by
Hansel Ivander
• 0
1
vote
3
replies
337
views
gnomAD4.0 Hail Table Downloading
NGS
gnomAD
updated 22 days ago by
Ram
41k • written 22 days ago by
adarsh_pp
▴ 30
0
votes
3
replies
335
views
RNA star taking more than 24h to complete 2nd pass
rna-seq
star
updated 23 days ago by
Ram
41k • written 23 days ago by
manuelmourato25
• 0
1
vote
2
replies
332
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 21 days ago by
Hongjin
• 0 • written 9 weeks ago by
mateomejias
• 0
0
votes
3
replies
328
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 11 days ago by
jv
★ 1.3k • written 17 days ago by
TC_Chang
▴ 10
0
votes
4
replies
326
views
Query regarding callsets used as known sites in Variant Calling
GATK
VCF
20 days ago by
Shruti Baikerikar
• 0
2
votes
3
replies
325
views
Selecting a subset of MSigDB database for GSEA
fgsea
clusterprofiler
GSEA
23 days ago by
Orange
▴ 10
1
vote
5
replies
323
views
vcftools
vcftools
updated 5 days ago by
Barista
▴ 10 • written 5 days ago by
sevda
• 0
0
votes
3
replies
323
views
Annovar - Annotated file cells show string
annovar
15 days ago by
Roshan
• 0
1
vote
4
replies
318
views
Analyze with Geo2R
R
NCBI
15 days ago by
anasjamshed
▴ 120
0
votes
3
replies
316
views
Appropriate genome reference for converting TCGA VCF files to MAF
maf
vcf
vcf2maf
TCGA
updated 21 days ago by
Zhenyu Zhang
★ 1.1k • written 25 days ago by
melissachua90
▴ 50
0
votes
3
replies
315
views
Can FPKM be used to create bar graphs for DEGs?
RNA-seq
updated 5 days ago by
Ram
41k • written 23 days ago by
junli1988
• 0
2
votes
2
replies
314
views
DESeq2 installation failures
DEseq2
updated 20 days ago by
Michael
53k • written 22 days ago by
dantuluri
• 0
1
vote
2
replies
311
views
featureCounts error???
featureCounts
error
updated 27 days ago by
Gordon Smyth
★ 6.5k • written 28 days ago by
Samer
• 0
0
votes
1
reply
308
views
EBI ArrayExpress
EBI
database
updated 26 days ago by
sil_bioinfo
▴ 40 • written 13 months ago by
haiying.kong
▴ 360
336 results • Page
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136k
> SPAdes wants interlaced fastq and BWA-MEM wants interleaved fastq Both programs will accept separate paired-end files. The reads in the …
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3.8k
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they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for…
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Sorry I accidentally hit enter BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to com…
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how about using the bed file of your targets....
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