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817 results • Page
4 of 17
Sort: replies
Rank
Views
Votes
Replies
2
votes
6
replies
202
views
gatk SelectVariants is giving dupilicate allele error while extracting SNPs out of vcf file
SNP
variantcalling
gatk
3 hours ago by
analyst
▴ 10
13
votes
6
replies
372
views
6 follow
how to sort fasta file according to a header file
fasta
updated 16 days ago by
Ram
41k • written 16 days ago by
Nelo
▴ 20
3
votes
6
replies
440
views
how extract information from the output text file?
R
linux
29 days ago by
satva72
• 0
7
votes
6
replies
1.1k
views
How does 10x Genomics 3' single cell data have reads aligning to exons that aren't terminal?
single-nucleus
rna-seq
igv
single-cell
updated 17 days ago by
Ram
41k • written 9 months ago by
kenneditodd
▴ 40
0
votes
6
replies
366
views
Resolving over clustered NGS with Q-scores
NGS
phred
Q-score
overclustering
1 day ago by
sam.himes92
• 0
1
vote
6
replies
270
views
Multi-factor designs in DiffBind
Chipseq
Multi-factor
Diffbind
updated 18 hours ago by
Rory Stark
★ 2.0k • written 1 day ago by
g.persic1991
• 0
14
votes
6
replies
6.0k
views
What Tool Should I Use To Assemble Data Produced By A 454 Sequencer?
assembly
next-gen-sequencing
updated 24 days ago by
Ram
41k • written 13.6 years ago by
Cupton
▴ 80
2
votes
6
replies
447
views
Filter a BED file based on genome coordinates for gene names
BED
GTF
GFF
updated 24 days ago by
Ram
41k • written 25 days ago by
joker
• 0
4
votes
6
replies
487
views
how to count the number of reads align per viruses in my sample
RNAseq
samtools
illumina
updated 23 days ago by
GenoMax
136k • written 24 days ago by
viviane20
• 0
6
votes
6
replies
440
views
6 follow
STAR alignment speed
STAR
alignment
RNA
updated 16 days ago by
ATpoint
78k • written 18 days ago by
Gilles
• 0
30
votes
6
replies
13k
views
What Are Some Good Free Bioinformatics And Computational Biology Books?
books
online
updated 24 days ago by
Ram
41k • written 13.6 years ago by
hadasa
★ 1.0k
4
votes
6
replies
2.9k
views
Gene Similarity Search
conservation
similarity
updated 24 days ago by
Ram
41k • written 13.7 years ago by
bow
▴ 790
4
votes
6
replies
560
views
Handling multiple fastq files per sample, per lane, per read out of the Cellranger bam to fastq workflow
bamtofastq
cellranger
RNA-seq
22 days ago by
Erfanesi
• 0
4
votes
6
replies
475
views
From TPM to raw counts
tpm
Deconvolution
rnaseq
5 days ago by
Gama313
▴ 120
6
votes
6
replies
453
views
6 follow
How to align a genome fasta file from NCBI to a reference genome?
genome
genetics
alignment
updated 16 days ago by
Antonio R. Franco
★ 5.1k • written 16 days ago by
ritafonsa
• 0
7
votes
5
replies
346
views
bcftools error: : error while loading shared libraries: libcrypto.so.1.0.0:
bcftools
14 days ago by
jiyoung
▴ 20
1
vote
5
replies
1.5k
views
BLAST: overflow error
BLAST
updated 4 days ago by
GenoMax
136k • written 19 months ago by
antoinefelden
▴ 60
5
votes
5
replies
6.2k
views
6 follow
Mitochondrial genes in single cell nuclear RNAseq data
RNA-Seq
gene
mitochondria
updated 14 days ago by
Prakki Rama
★ 2.7k • written 4.9 years ago by
dalhoomist
▴ 40
8
votes
5
replies
4.4k
views
Exon Array Analysis Tools
gene
microarray
updated 27 days ago by
Ram
41k • written 13.7 years ago by
Chris Miller
22k
5
votes
5
replies
346
views
salmon for gene expression quantification
salmon
gene-expression
updated 22 days ago by
dsull
★ 5.1k • written 22 days ago by
Ashish
• 0
7
votes
5
replies
1.4k
views
How to learn Scanpy
scanpy
Python
rna-seq
updated 14 days ago by
Prakki Rama
★ 2.7k • written 17 months ago by
godwin
▴ 30
0
votes
5
replies
345
views
HTseq reports missing attribute name
htseq
updated 8 days ago by
Istvan Albert
99k • written 10 days ago by
Bjorn
• 0
4
votes
5
replies
1.7k
views
PyMOL: Gaps in protein structure yet shown by the sequence
PyMOL
structure
protein
updated 11 days ago by
pippo1980
• 0 • written 10 months ago by
spence.lank
▴ 10
0
votes
5
replies
303
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
updated 3 days ago by
manaswwm
▴ 490 • written 8 days ago by
J
• 0
1
vote
5
replies
383
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
updated 1 day ago by
Rory Stark
★ 2.0k • written 9 days ago by
DINESHR
• 0
2
votes
5
replies
245
views
kallisto index build difference according to version
index
version
kallisto
updated 4 days ago by
dsull
★ 5.1k • written 4 days ago by
estilo
• 0
1
vote
5
replies
661
views
ATAC-Seq and RPKM
RPKM
ATAC-Seq
updated 2 days ago by
ATpoint
78k • written 9 weeks ago by
qudrat.nii
• 0
6
votes
5
replies
386
views
Calculate GC content for entire chromosome
bam
GC
assembly
bwa-mem
updated 1 day ago by
colindaven
5.8k • written 2 days ago by
skilleta0527
• 0
2
votes
5
replies
639
views
Genome coverage of MAGs while submitting to NCBI
genome
MAGs
coverage
metagenomics
updated 18 hours ago by
Mensur Dlakic
★ 25k • written 3 months ago by
Konstantin
• 0
1
vote
5
replies
865
views
Strandedness of RNA-seq results
dual-RNA-seq
featurecounts
strandedness
HISAT2
updated 2 days ago by
charles.feigin
• 0 • written 19 months ago by
jamesymtang
▴ 10
0
votes
5
replies
562
views
Lack of correspondance of GFA node IDs to giraffe/call node IDs
giraffe
pggb
vg
updated 10 days ago by
Wenhai
• 0 • written 7 weeks ago by
javierbelmor
• 0
6
votes
5
replies
3.1k
views
Multi threading bowtie index
bowtie
indexing
updated 13 days ago by
colindaven
5.8k • written 8.3 years ago by
ChillarAnand
▴ 70
2
votes
5
replies
329
views
Abyss results
assembly
abyss
25 days ago by
erikatatianacs
• 0
5
votes
5
replies
1.8k
views
GSEA for RNA_seq dataset
DEGs
GSEA
RNA-seq
updated 2 days ago by
Ram
41k • written 2.6 years ago by
1961012
▴ 20
0
votes
5
replies
161
views
Differential expression using Bowtie2
Transcriptome
Bowtie
Differential-expression
updated 22 minutes ago by
ATpoint
78k • written 19 hours ago by
8d8fc19e
• 0
3
votes
5
replies
531
views
Circular genome browser
genome-browser
circular-genome
updated 9 days ago by
cmdcolin
★ 3.4k • written 5 weeks ago by
giammafer
▴ 20
8
votes
5
replies
2.4k
views
Convert FPKM to TPM in R
meta-analysis
TPM
r
normalization
updated 20 days ago by
Ram
41k • written 14 months ago by
JACKY
▴ 120
0
votes
5
replies
391
views
How to deeply sequence long inserts
NGS
phage
read
display
Long
updated 9 days ago by
GenoMax
136k • written 9 days ago by
Ryan
• 0
2
votes
5
replies
362
views
FastQC without yellow box
fastqc
updated 2 days ago by
Ram
41k • written 3 days ago by
lobelino
• 0
1
vote
5
replies
342
views
bcftools mipileup error: format error, unexpected A at line 1
bcftools
updated 24 days ago by
Jautis
▴ 520 • written 25 days ago by
jiyoung
▴ 20
0
votes
5
replies
406
views
Three questions about datasets
geo
datasets
sra
18 days ago by
SHXVRR
▴ 20
0
votes
5
replies
537
views
Job:
Tutor Needed
genomes
mosquitoes
nanopore
metagenomics
28 days ago by
doppelganger1030
• 0
16
votes
5
replies
12k
views
Where Can I Find The Basepair Positions Of Chromosome Bands?
chromosome
position
updated 6 days ago by
Malachi Griffith
19k • written 13.2 years ago by
Abdel
▴ 370
13
votes
5
replies
6.8k
views
How To Align Reads Obtained From Sequence Capture
exome-sequencing
next-gen-sequencing
sequence
updated 24 days ago by
Ram
41k • written 13.6 years ago by
Istvan Albert
99k
5
votes
5
replies
394
views
6 follow
Finding exons that are always included
alternative-splicing
exon
updated 29 days ago by
Jeremy Leipzig
22k • written 29 days ago by
smurph50
▴ 50
5
votes
5
replies
397
views
Using metagenome assembly and binning to identify and mitigate contamination in a genome
genomes
contamination
metagenomics
3 days ago by
btc347
• 0
0
votes
5
replies
460
views
bam file missing barcode and UMI info
barcode
star
starsolo
updated 28 days ago by
GenoMax
136k • written 4 weeks ago by
malonzm1
• 0
1
vote
5
replies
312
views
vcftools
vcftools
updated 3 days ago by
Barista
▴ 10 • written 3 days ago by
sevda
• 0
1
vote
5
replies
379
views
How can I map coordinates between two strains of yeast?
coordinates
yeast
genome
mapping
fasta
7 days ago by
Jimmy
▴ 10
2
votes
5
replies
715
views
Pre-processing for Agilent microarray data?
affymetrix
microarray
gene
agilent
rna
updated 21 days ago by
1769mkc
★ 1.1k • written 6 months ago by
survive
• 0
817 results • Page
4 of 17
Recent Votes
Comment: Normalization of RNA captureSeq data (<20 genes captured)
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Comment: gatk SelectVariants is giving dupilicate allele error while extracting SNPs out
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158k
run a `system()` command from R ?
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Check how many variants you have without filtering for MAF, maybe use a MAF of 0.01? You could try the --impute-sex **ycount** or **y-only*…
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Thanks @Pierre this is great to know, although it doesn't solve my issue of this being R-self-contained. rsamtools doesn't seem to carry fu…
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Ok, thanks for letting me know. What would you do if you wanted to compare differential expression of a gene across tissues from RNA-seq da…
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What is the question exactly? With only 20 genes you basically **must** use the spike-ins as that few genes do not really allow to normaliz…
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analyst
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Its bbmap tool callvariants.sh. I think you are right because I did not get such error when I called variants through freebayes.
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Please contact the UniProt helpdesk whenever you find such annotations, especially in these cases where the GO evidence/source tag says "Un…
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