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1,000 results • Page
2 of 20
Sort: Views
Rank
Views
Votes
Replies
0
votes
3
replies
13k
views
edgeR: likelihood ratio test or quasi-likelihood F-test?
R
rna-seq
next-gen
7.0 years ago by
moxu
▴ 510
4
votes
9
replies
13k
views
Seqtk subseq: structure of file name.lst
sequence
next-gen
updated 5.9 years ago by
Ram
43k • written 5.9 years ago by
ste.lu
▴ 80
2
votes
4
replies
12k
views
Run BLAST on Linux terminal
ncbi
nBLAST
linux
blast
updated 18 months ago by
Ram
43k • written 8.5 years ago by
Abdul Rafay Khan
★ 1.2k
2
votes
13
replies
12k
views
8 follow
(ERR): bowtie2-align exited with value 1
software error
RNA-Seq
updated 6.2 years ago by
basucsmcri
• 0 • written 7.1 years ago by
biostarsb
▴ 30
0
votes
1
reply
12k
views
PLINK 1.9 - Converting PED/MAP to BED/BIM/FAM with missing values
plink
updated 7.7 years ago by
Biostar
20 • written 7.7 years ago by
rednalf
▴ 90
16
votes
7
replies
12k
views
8 follow
MAF vs VAF
sequencing
updated 3 days ago by
Ömer An
▴ 260 • written 6.0 years ago by
lauren.wahyudi
▴ 50
41
votes
55
replies
12k
views
6 follow
hash function for DNA sequences
hash
hashing
DNA
8.0 years ago by
midox
▴ 290
3
votes
2
replies
12k
views
ExAC PLI score calculation
DNA-Seq
7.1 years ago by
jonessara770
▴ 240
3
votes
8
replies
12k
views
6 follow
How do I go from UniProt ID to retrieving the gene name?
sequence
6.4 years ago by
a.rex
▴ 350
7
votes
9
replies
12k
views
Different alignment rates for Hisat2 and STAR, Hisat2 has lower alignment rate and STAR have many multi aligned reads
RNA-Seq
updated 6.5 years ago by
Satyajeet Khare
★ 1.6k • written 6.5 years ago by
SMILE
▴ 170
2
votes
13
replies
12k
views
MarkDuplicates memory issue
alignment
Picard
MarkDuplicates
8.2 years ago by
cacampbell
▴ 60
8
votes
5
replies
12k
views
samtools tview symbols
samtools
updated 17 months ago by
Ram
43k • written 8.7 years ago by
biolab
★ 1.4k
6
votes
7
replies
12k
views
bedtools intersect bed and vcf, coordinates problem
bedtools
bed
vcf
7.0 years ago by
abascalfederico
★ 1.2k
0
votes
3
replies
12k
views
Extracting Specific Columns from Multiple Files & Writing to File Python
python
file-handeling
7.9 years ago by
BioICoder
▴ 40
3
votes
4
replies
12k
views
basename: missing operand
snp
4.7 years ago by
evelyn
▴ 220
0
votes
4
replies
11k
views
Convert .gbf file to .gbk or .gff
gbk
gff
gbf
updated 14 months ago by
Ram
43k • written 8.9 years ago by
che.bellaj
• 0
3
votes
16
replies
11k
views
combining z-scores into a single z-score value
excel
R
statistics
updated 10 months ago by
Ram
43k • written 5.0 years ago by
Star
▴ 60
1
vote
2
replies
11k
views
Downloading BAM files GEO/SRA
bam
sra
geo
samtools
sratoolkit
7.7 years ago by
ilobelo
▴ 10
2
votes
3
replies
11k
views
converting maf to vcf
Exome
maf2vcf
updated 14 months ago by
Ram
43k • written 8.9 years ago by
ashishchahl
• 0
4
votes
14
replies
11k
views
All the reads aligned using STAR have low mapping quality (0-3). What is happening?
mapping quality
STAR
BWA
alignment
7.7 years ago by
kirannbishwa01
★ 1.6k
3
votes
4
replies
11k
views
Zlib.Error: -3 While Decompressing: Invalid Distance To Far Back (By Using Macs For Chip-Seq Data)
error
12.5 years ago by
Lisanne
• 0
4
votes
7
replies
11k
views
Grab Coordinate Of Centromeres From Ucsc
ucsc
10.9 years ago by
jeansimon32
▴ 170
2
votes
8
replies
11k
views
Loading Custom Genome In Igv Is Not Displaying Genes, Names Match.
igv
gff
reference
contigs
12.1 years ago by
Nickengland
▴ 130
2
votes
4
replies
11k
views
Pymol-Generate Pymol Movie To Mpeg
pymol
updated 2.2 years ago by
Ram
43k • written 12.2 years ago by
Reyhaneh
▴ 530
5
votes
9
replies
11k
views
Error with samtools faidx...Different line length in sequence
samtools
faidx
updated 5.9 years ago by
Biostar
20 • written 6.0 years ago by
oars
▴ 200
2
votes
0
replies
11k
views
How to plot UniFrac PCoA with 95% confidence Elipses in R
metagenomics
ordiellipse
vegan
R
phyloseq
updated 2.0 years ago by
Ram
43k • written 9.2 years ago by
c.v.oflynn
▴ 100
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch effects
updated 6.5 years ago by
Biostar
20 • written 6.7 years ago by
lessismore
★ 1.3k
7
votes
8
replies
11k
views
Picard tools duplicate removal
RNA-Seq
picard-tools
6.5 years ago by
blur
▴ 280
6
votes
3
replies
11k
views
Sequence duplication levels-RNA Seq
RNA-Seq
updated 3.5 years ago by
joshua.theisen
▴ 30 • written 6.0 years ago by
makwana.kd
▴ 50
3
votes
1
reply
10k
views
Negative P-Values
gene
genome
next-gen-sequencing
updated 19 months ago by
Ram
43k • written 8.6 years ago by
stevenlang123
▴ 210
4
votes
11
replies
10k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF
snp
19 months ago by
prasundutta87
▴ 660
2
votes
2
replies
10k
views
How to make clusters in heat map using ggplot2?
RNA-Seq
rna-seq
R
4.9 years ago by
John
▴ 270
3
votes
6
replies
10k
views
6 follow
How to calculate genetic correlation with R
R
updated 22 months ago by
ibomsolomon
• 0 • written 9.9 years ago by
Tohamy
▴ 80
3
votes
2
replies
10k
views
BWA-MEM Vs BWA-ALN
next-gen
genome
alignment
7.9 years ago by
SOHAIL
▴ 400
11
votes
10
replies
10k
views
Extracting from tophat outputs reads pairs and splice-junctions with a single best match
TOPHAT
RNA-Seq
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
trakhtenberg
▴ 160
0
votes
0
replies
10k
views
pheatmap row annotation and title font size questions
heatmap
pheatmap
updated 14 months ago by
Ram
43k • written 8.9 years ago by
neokao
• 0
2
votes
1
reply
10k
views
Calculate Linkage Disequilibrium For Snps (Using R^2)
snp
linkage
10.7 years ago by
TitoPullo
▴ 180
1
vote
2
replies
10k
views
Converting MSTRG from stringtie with gene name
RNA-Seq
Stringtie
updated 6.2 years ago by
Biostar
20 • written 6.2 years ago by
fhassanz
▴ 20
5
votes
2
replies
10k
views
Turning Seq objects into strings
sequence
5.0 years ago by
schlogl
▴ 160
2
votes
8
replies
10k
views
Plotting different gene ontology categories in a barplot
HI
Gene ontology
R
updated 20 months ago by
zx8754
11k • written 3.1 years ago by
aradhana
• 0
7
votes
9
replies
10k
views
Samtools Index Segmentation Fault
samtools
index
10.0 years ago by
Noushin N
▴ 600
0
votes
1
reply
10k
views
Is it normal that nearly all of p-value is equal to 0.1 in PERMANOVA analysis
PERMANOVA
statistics
metagenomics
updated 3.3 years ago by
dqq102829
• 0 • written 4.2 years ago by
zhangdengwei
▴ 210
2
votes
8
replies
10k
views
Size of typical genomic data
genomic
updated 12 months ago by
Ram
43k • written 5.9 years ago by
Nicolas Rosewick
10k
1
vote
7
replies
10k
views
How to find up-regulated and down-regulated genes after GEO2R analysis?
GEO
genes
up-regulated
down-regulated
GEO2R
6.1 years ago by
DanielC
▴ 160
0
votes
0
replies
10k
views
Map Between Uniprot Accesion And Gene.Symbol Using R Or/And Mysql
r
bioconductor
mysql
10.2 years ago by
jfertaj
▴ 110
1
vote
5
replies
10k
views
What Agilent Interval Files (.Bed) Should I Use For Exome Variant Calling With Gatk?
bed
agilent
gatk
updated 4.1 years ago by
Karma
▴ 310 • written 10.3 years ago by
newDNASeqer
▴ 760
3
votes
3
replies
10k
views
bcftools mpileup output format
bcftools
mpileup
5.6 years ago by
tarek.mohamed
▴ 360
2
votes
4
replies
10k
views
num_threads with blastn in blast 2.6.0+
blast
5.3 years ago by
navela78
▴ 70
3
votes
4
replies
10k
views
Aligning RNA seq data to genome or transcriptome
RNA-Seq
ngs
transcriptome
genome
updated 6.6 years ago by
Ram
43k • written 6.6 years ago by
KVC_bioinfo
▴ 590
1
vote
1
reply
10k
views
Raxml bootstrap support values
figtree
raxml
bootstrap
updated 2.5 years ago by
Ram
43k • written 9.9 years ago by
JackBel
• 0
1,000 results • Page
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Recent Votes
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Synthetic lethality and cancer database
Answer: log2(TPM+1)
Comment: Error in openning FastQC
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Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Answer: Is RNAseq data from a monoclonal cell line technically considered scRNAseq?
by
Soheil
▴ 90
Bulk RNAseq from any sample is still considered a bulk sample. Running bulk RNA sequencing on a sample with any level of cell type/state c…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
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by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
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Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
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GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
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Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
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friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
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GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
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