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1,000 results • Page
2 of 20
Sort: Views
Rank
Views
Votes
Replies
0
votes
3
replies
11k
views
Extracting Specific Columns from Multiple Files & Writing to File Python
python
file-handeling
7.0 years ago by
BioICoder
▴ 40
3
votes
2
replies
11k
views
ExAC PLI score calculation
DNA-Seq
6.3 years ago by
jonessara770
▴ 240
0
votes
3
replies
11k
views
edgeR: likelihood ratio test or quasi-likelihood F-test?
R
rna-seq
next-gen
6.1 years ago by
moxu
▴ 500
7
votes
9
replies
11k
views
Different alignment rates for Hisat2 and STAR, Hisat2 has lower alignment rate and STAR have many multi aligned reads
RNA-Seq
updated 5.7 years ago by
Satyajeet Khare
★ 1.6k • written 5.7 years ago by
SMILE
▴ 170
8
votes
5
replies
11k
views
samtools tview symbols
samtools
updated 6 months ago by
Ram
39k • written 7.9 years ago by
biolab
★ 1.4k
2
votes
13
replies
11k
views
8 follow
(ERR): bowtie2-align exited with value 1
software error
RNA-Seq
updated 5.3 years ago by
basucsmcri
• 0 • written 6.3 years ago by
biostarsb
▴ 30
3
votes
4
replies
11k
views
Zlib.Error: -3 While Decompressing: Invalid Distance To Far Back (By Using Macs For Chip-Seq Data)
error
11.7 years ago by
Lisanne
• 0
4
votes
7
replies
11k
views
Grab Coordinate Of Centromeres From Ucsc
ucsc
10.0 years ago by
jeansimon32
▴ 160
4
votes
9
replies
11k
views
Seqtk subseq: structure of file name.lst
sequence
next-gen
updated 5.1 years ago by
Ram
39k • written 5.1 years ago by
ste.lu
▴ 80
0
votes
4
replies
11k
views
Convert .gbf file to .gbk or .gff
gbk
gff
gbf
updated 4 months ago by
Ram
39k • written 8.0 years ago by
che.bellaj
• 0
1
vote
13
replies
11k
views
"[E::bgzf_read] Read block operation failed" error - possible truncation/corruption of BAM file
samtools
updated 2.0 years ago by
darklings
▴ 520 • written 3.6 years ago by
gordo2b
• 0
2
votes
3
replies
11k
views
converting maf to vcf
Exome
maf2vcf
updated 4 months ago by
Ram
39k • written 8.0 years ago by
ashishchahl
• 0
3
votes
8
replies
11k
views
6 follow
How do I go from UniProt ID to retrieving the gene name?
sequence
5.5 years ago by
a.rex
▴ 350
1
vote
13
replies
10k
views
MarkDuplicates memory issue
alignment
Picard
MarkDuplicates
7.4 years ago by
cacampbell
▴ 50
1
vote
2
replies
10k
views
Downloading BAM files GEO/SRA
bam
sra
geo
samtools
sratoolkit
6.8 years ago by
ilobelo
▴ 10
2
votes
4
replies
10k
views
Pymol-Generate Pymol Movie To Mpeg
pymol
updated 16 months ago by
Ram
39k • written 11.3 years ago by
Reyhaneh
▴ 530
13
votes
6
replies
10k
views
6 follow
MAF vs VAF
sequencing
5.2 years ago by
lauren.wahyudi
▴ 40
3
votes
1
reply
10k
views
Negative P-Values
gene
genome
next-gen-sequencing
updated 9 months ago by
Ram
39k • written 7.7 years ago by
stevenlang123
▴ 200
2
votes
0
replies
10k
views
How to plot UniFrac PCoA with 95% confidence Elipses in R
metagenomics
ordiellipse
vegan
R
phyloseq
updated 14 months ago by
Ram
39k • written 8.4 years ago by
c.v.oflynn
▴ 100
41
votes
55
replies
10k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
7.2 years ago by
midox
▴ 290
2
votes
8
replies
10k
views
Loading Custom Genome In Igv Is Not Displaying Genes, Names Match.
igv
gff
reference
contigs
11.3 years ago by
Nickengland
▴ 130
2
votes
1
reply
10k
views
Calculate Linkage Disequilibrium For Snps (Using R^2)
snp
linkage
9.9 years ago by
TitoPullo
▴ 180
7
votes
8
replies
10.0k
views
Picard tools duplicate removal
RNA-Seq
picard-tools
5.6 years ago by
blur
▴ 270
6
votes
7
replies
9.9k
views
bedtools intersect bed and vcf, coordinates problem
bedtools
bed
vcf
6.1 years ago by
abascalfederico
★ 1.2k
1
vote
8
replies
9.9k
views
How to update rlang in R?
rlang
R
7 months ago by
Amr
▴ 140
4
votes
14
replies
9.9k
views
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
mapping quality
STAR
BWA
alignment
6.8 years ago by
kirannbishwa01
★ 1.5k
3
votes
16
replies
9.9k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 5 hours ago by
Ram
39k • written 4.2 years ago by
Star
▴ 60
11
votes
10
replies
9.8k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 17 months ago by
Ram
39k • written 8.8 years ago by
trakhtenberg
▴ 160
1
vote
2
replies
9.8k
views
Converting MSTRG from stringtie with gene name
RNA-Seq
Stringtie
updated 5.4 years ago by
Biostar
20 • written 5.4 years ago by
fhassanz
▴ 20
1
vote
1
reply
9.8k
views
Raxml bootstrap support values
figtree
raxml
bootstrap
updated 20 months ago by
Ram
39k • written 9.0 years ago by
JackBel
• 0
3
votes
2
replies
9.8k
views
BWA-MEM Vs BWA-ALN
next-gen
genome
alignment
7.0 years ago by
SOHAIL
▴ 400
0
votes
0
replies
9.8k
views
Map Between Uniprot Accesion And Gene.Symbol Using R Or/And Mysql
r
bioconductor
mysql
9.4 years ago by
jfertaj
▴ 110
0
votes
1
reply
9.7k
views
Is it normal that nearly all of p-value is equal to 0.1 in PERMANOVA analysis
PERMANOVA
statistics
metagenomics
updated 2.4 years ago by
dqq102829
• 0 • written 3.4 years ago by
zhangdengwei
▴ 180
1
vote
5
replies
9.6k
views
What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With Gatk?
bed
agilent
gatk
updated 3.3 years ago by
Karma
▴ 310 • written 9.5 years ago by
newDNASeqer
▴ 750
3
votes
4
replies
9.6k
views
basename: missing operand
snp
3.9 years ago by
evelyn
▴ 220
7
votes
9
replies
9.5k
views
Samtools Index Segmentation Fault
samtools
index
9.2 years ago by
Noushin N
▴ 600
3
votes
9
replies
9.5k
views
Error with samtools faidx...Different line length in sequence
samtools
faidx
updated 5.0 years ago by
Biostar
20 • written 5.2 years ago by
oars
▴ 190
2
votes
16
replies
9.5k
views
Tophat with Bowtie2 long index
tophat
bowtie
updated 17 months ago by
Ram
39k • written 8.9 years ago by
BDK_compbio
▴ 130
0
votes
0
replies
9.5k
views
pheatmap row annotation and title font size questions
heatmap
pheatmap
updated 4 months ago by
Ram
39k • written 8.0 years ago by
neokao
• 0
3
votes
6
replies
9.4k
views
6 follow
How to calculate genetic correlation with R
R
updated 12 months ago by
ibomsolomon
• 0 • written 9.1 years ago by
Tohamy
▴ 80
2
votes
2
replies
9.4k
views
How to make clusters in heat map using ggplot2?
RNA-Seq
rna-seq
R
4.1 years ago by
John
▴ 270
2
votes
8
replies
9.3k
views
Size of typical genomic data
genomic
updated 9 weeks ago by
Ram
39k • written 5.0 years ago by
Nicolas Rosewick
10k
3
votes
10
replies
9.2k
views
How can I obtain SNP from TCGA?
Risky-allele
BRCA
SNP
updated 17 months ago by
Ram
39k • written 8.7 years ago by
purmod
▴ 10
13
votes
22
replies
9.2k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 5.7 years ago by
Biostar
20 • written 5.9 years ago by
lessismore
★ 1.3k
2
votes
2
replies
9.1k
views
Imputation Analysis In Plink?
plink
gwas
imputation
11.3 years ago by
Davy
▴ 210
0
votes
2
replies
9.1k
views
DESeq2 pheatmap returns Error in check.length("fill") : 'gpar' element 'fill' must not be length 0
RNA-Seq
DESeq2
gpar
pheatmap
5.6 years ago by
Anthony.Knox
▴ 60
4
votes
2
replies
9.0k
views
Hisat2 versus Bowtie2
Exome-sequencing
hisat2
bowtie2
updated 5.9 years ago by
Biostar
20 • written 7.1 years ago by
nalpas.nicolas
▴ 20
3
votes
4
replies
8.9k
views
Aligning RNA seq data to genome or transcriptome
RNA-Seq
ngs
transcriptome
genome
updated 5.7 years ago by
Ram
39k • written 5.7 years ago by
KVC_bioinfo
▴ 570
1
vote
4
replies
8.9k
views
R ggplot Align Y-Axis on multiple graphs
ggarrange
ggplot2
r
updated 3.8 years ago by
Biostar
20 • written 5.3 years ago by
jjrin
▴ 40
0
votes
8
replies
8.9k
views
how to find a read by name in a bam file
next-gen
sequencing
Tool
updated 5.9 years ago by
Samuel Brady
▴ 320 • written 5.9 years ago by
himanimalhotra89
• 0
1,000 results • Page
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Comment: Regular Expression for conversion
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Comment: Unusual FASTQ file
by
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39k
People from the middle east/indian subcontinent often associate the term "post title" with their job title, because a) post translates more…
Comment: How to make a dotplot for bulk RNA average expression ?
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I am not entirely clear on what you are trying to accomplish, but based on @Trivas answer, I would first transform the data relative to ave…
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13k
There really is no "best". Just find something reasonable, and document what you chose.
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ok interesting. Do all, most, some, or a few of the genes have repeated lines. Is there a handy link to the exact file you are looking at?
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Bedtools window piped into genomecov? https://bedtools.readthedocs.io/en/latest/content/tools/window.html https://bedtools.readthedocs.io…
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72k
STAR counts are the raw counts, that is appropriate for DESeq2.
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by
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13k
STAR has a GeneCounts output that looks as you describe; three columns, depending on whether one thinks the prep is unstranded, or stranded…
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by
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39k
There is at least one more step that you haven't shared, isn't there? This line alone does not get you the data. You don't need to give us …
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by
turcoa1
• 0
my entire code is not done. All I am trying to understand is if the STAR - counts downloaded from this query have raw reads. There are head…
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by
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39k
Please provide your entire code so those of us wishing to do a quick test can download and check for ourselves. Also, please use the format…
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by
turcoa1
• 0
```r query <- GDCquery( project = "TCGA-THCA", data.category = "Transcriptome Profiling", data.type = "Gene Expression Quantificatio…
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by
GenoMax
129k
It may be best to email NCBI help desk with these questions. Post their response here once you hear back from them.
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39k
What data are you downloading? Can you show us your GDCquery commands please?
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129k
> I am using the Bos Taurus files Which organism are you actually working on? You have mentioned three so far, arabidopsis, human and now …
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