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1,000 results • Page
6 of 20
Sort: Votes
Rank
Views
Votes
Replies
8
votes
7
replies
5.9k
views
Download human 3 UTR FASTA file
genome
8.2 years ago by
bharata1803
▴ 560
7
votes
5
replies
9.5k
views
strange issues with absent EOF markers in BAM files
samtools
picard-tools
bam
eof
7.9 years ago by
abascalfederico
★ 1.2k
7
votes
8
replies
11k
views
Picard tools duplicate removal
RNA-Seq
picard-tools
6.6 years ago by
blur
▴ 280
7
votes
6
replies
4.1k
views
Low percentage of reads in Tophat, Is the any setting to improve?
Tophat
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
Leandro de Mattos
▴ 90
7
votes
4
replies
1.5k
views
So many Zeros (read counting)_NGS sequence analysis with R / Bioconductor: RNA-Seq workflow
alignment
RNA-Seq
R
updated 14 months ago by
Ram
43k • written 5.9 years ago by
healing80
• 0
7
votes
8
replies
1.1k
views
What sequencing read aligners other than RazerS guarantee full sensitivity?
alignment
sequence
5.9 years ago by
adam.nunn
• 0
7
votes
7
replies
3.0k
views
LRT test with DESeq2 and how to interpret the results
significant
LRT
DESeq2
genes
RNA-Seq
updated 22 months ago by
1769mkc
★ 1.2k • written 2.0 years ago by
Maka
▴ 20
7
votes
5
replies
1.7k
views
best programs for alignment of large whole genomes?
Assembly
alignment
genome
5.7 years ago by
vulpecula
▴ 30
7
votes
4
replies
5.9k
views
How to extract reads which contain specific sequence from fastq file
fastq
reads
extract
updated 5.0 years ago by
WouterDeCoster
47k • written 5.0 years ago by
hsu
▴ 40
7
votes
12
replies
8.1k
views
How to identify ORFs in Python dictionaries
Python3
ORF
Open reading frame
python dictionaries
7.3 years ago by
ron
▴ 40
7
votes
13
replies
4.1k
views
DESeq2: can I correct for relatedness when using data from multiplex families?
DESeq2
RNA-Seq
Multiplex-families
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
alesssia
▴ 580
7
votes
9
replies
3.4k
views
bowtie-2 build error
bowtie2-build error
6.9 years ago by
NGS-Newbie
▴ 10
7
votes
2
replies
4.4k
views
How To Get Gap Positions From Genome Fasta File
genome
fasta
position
12.1 years ago by
creepycomputing
▴ 40
7
votes
6
replies
1.7k
views
Solutions to FastQC diagnosis of Micro-Satellites
fastqc
RNA-Seq
6.5 years ago by
dec986
▴ 380
7
votes
15
replies
7.2k
views
6 follow
blastn error - NCBI C++ Exception
assembly
blast
alignment
updated 2.1 years ago by
lieven.sterck
15k • written 3.1 years ago by
sunnykevin97
▴ 980
7
votes
4
replies
4.4k
views
IGV genome browser problems
igv
updated 17 months ago by
Ram
43k • written 8.9 years ago by
Marvin
▴ 220
7
votes
9
replies
1.9k
views
Possible reasons mapping percentage abysmally low for miRNA reads?
miRNA
miRDeep2
4.3 years ago by
VBer
▴ 200
7
votes
16
replies
4.0k
views
cutting overrepresented sequences (recognized by fatsqc)
sequencing
genome-sequence
fastqc
genome
sequence
4.1 years ago by
Researcher
▴ 20
7
votes
4
replies
4.2k
views
Calculating fold change
genome
updated 6.9 years ago by
Biostar
20 • written 7.1 years ago by
amir.007.taherkhani
▴ 10
7
votes
2
replies
5.3k
views
Store Structural Variants Into Vcf
vcf
11.2 years ago by
Tomáš Beluský
▴ 90
7
votes
8
replies
1.7k
views
fastq dump usage of microRNA-seq data
RNA-Seq
microRNA
fastq
4.9 years ago by
K.patel5
▴ 140
7
votes
10
replies
3.9k
views
Choosing phylogenetic approaches
phylogeny
updated 2.3 years ago by
Ram
43k • written 9.7 years ago by
Yongjie Zhang
▴ 110
7
votes
2
replies
2.2k
views
save plots in for loop
R
for loop
jpeg
grep
6.9 years ago by
mbk0asis
▴ 700
7
votes
10
replies
1.9k
views
Ubuntu 20.04 Crash
Ubuntu
updated 15 months ago by
Ram
43k • written 2.3 years ago by
bala
• 0
7
votes
7
replies
1.9k
views
Sort and convert the SAM files to BAM
samtools
RNA-seq
NGS
updated 8 months ago by
Ram
43k • written 5.8 years ago by
amitunited0532
▴ 40
7
votes
16
replies
2.8k
views
Insert size selection for RNASeq data: does it make sense?
RNA-Seq
sequencing
updated 13 months ago by
Ram
43k • written 6.6 years ago by
Matteo Schiavinato
★ 3.6k
7
votes
21
replies
3.2k
views
Merged.gtf vs. Rnor_6.0.gtf for Raw Counts
RNA-Seq
cuffmerge
raw counts
7.5 years ago by
jmsyl.hong
• 0
7
votes
11
replies
7.3k
views
HTSEq-Count returns 0 counts for all genes in the counts file!
RNA-Seq
htseq-count
6.3 years ago by
manish.nu
• 0
7
votes
11
replies
1.8k
views
(closed) Direction to take in presenting RNA-seq data
RNA-Seq
updated 6.1 years ago by
Biostar
20 • written 6.2 years ago by
Muha0216
• 0
7
votes
10
replies
3.0k
views
8 follow
Parsing Blast output on linux/unix
blast
parse
output
python
linux
updated 6.0 years ago by
shira.zaltsman
▴ 20 • written 6.0 years ago by
chagross
▴ 40
7
votes
10
replies
1.7k
views
SNP Data Quality control
SNP
R
updated 7.2 years ago by
Biostar
20 • written 7.2 years ago by
mms140130
▴ 60
7
votes
7
replies
2.1k
views
How to make a simple pipeline to identify the Reciprocal Best Hits for the subject genes
Reciprocal
Hits
Best
updated 2.2 years ago by
Dunois
★ 2.5k • written 2.2 years ago by
Teo
▴ 10
7
votes
10
replies
1.7k
views
col as names [solved]
R
updated 14 months ago by
Ram
43k • written 5.2 years ago by
demoraesdiogo2017
▴ 100
7
votes
8
replies
2.3k
views
bedops wig2bed 'Row begins with a tab or space' error
wig2bed
bedops
convert2bed
updated 3.1 years ago by
Alex Reynolds
35k • written 3.1 years ago by
a_bis
▴ 40
7
votes
5
replies
3.4k
views
How to merge quality trimmed interlaced reads?
RNA-Seq
updated 5.5 years ago by
Biostar
20 • written 6.1 years ago by
O.rka
▴ 720
7
votes
12
replies
3.3k
views
RNA secondary structure - Feature extraction
RNA secondary structure
Structural Fragments
6.0 years ago by
Manu Madhavan
▴ 20
7
votes
3
replies
7.1k
views
How to set a threshold for coefficient of variation in RNA-seq?
dispersion
statistics
single-cell
RNA-Seq
variance
updated 2.1 years ago by
Ram
43k • written 9.3 years ago by
gaelgarcia
▴ 270
7
votes
8
replies
2.9k
views
Discrepency between number of reads tophat
RNA-Seq
tophat
software-error
updated 19 months ago by
Ram
43k • written 8.7 years ago by
mbio.kyle
▴ 380
7
votes
10
replies
4.8k
views
PSMC using haploid genomes
haploid
genome
PSMC
updated 2.2 years ago by
Ram
43k • written 9.5 years ago by
biogirl
▴ 210
7
votes
3
replies
5.5k
views
Ensemble Identifier Of Mirna
mirna
gene-ontology
enrichment
analysis
bioinformatician
microarray
10.5 years ago by
khan
▴ 100
7
votes
9
replies
1.2k
views
Find a gene from RNA-seq data without GTF
RNA-Seq
4.2 years ago by
avino
▴ 20
7
votes
4
replies
2.0k
views
useful and freely available softwares for Bioinformatics
software
updated 14 months ago by
Ram
43k • written 9.2 years ago by
Mo
▴ 920
7
votes
1
reply
7.0k
views
createRepeatLandscape in RepeatMasker
RepeatMasker
7.7 years ago by
a.rex
▴ 350
7
votes
4
replies
2.1k
views
Different mappability/effective genome fraction with paired end reads? (ChIP-Seq)
ChIP-Seq
updated 7.6 years ago by
Biostar
20 • written 8.1 years ago by
endrebak
▴ 960
7
votes
5
replies
4.8k
views
Difference between Private SNPs and Singleton SNPs
SNPs
GATK
variant calling
SNP
population genetics
5.3 years ago by
prasundutta87
▴ 660
7
votes
6
replies
6.3k
views
Need Advice On The Correct Usage For The Genome Structure Correction Statistical Software From The Encode Project
statistics
enrichment
encode
updated 11.2 years ago by
Istvan Albert
100k • written 12.0 years ago by
Chris Whelan
▴ 570
7
votes
15
replies
4.3k
views
Biopython Pairwise Alignment output
biopython
needleman
global alignment
4.1 years ago by
tommaso.green
• 0
7
votes
2
replies
2.9k
views
protein interaction database
protein
database
interaction
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
yliueagle
▴ 290
7
votes
10
replies
4.4k
views
Transcriptome Assembly with rnaSPAdes
RNA-Seq
7.4 years ago by
biofalconch
★ 1.1k
7
votes
4
replies
2.2k
views
Error: missing values and NaN's not allowed if 'na.rm' is FALSE
Genome
Software
22 months ago by
sunnykevin97
▴ 980
1,000 results • Page
6 of 20
Recent Votes
Answer: Doubt about the process of annotation, detection, identification and classificat
Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
A: how to combine RNA seq data from 4 lanes
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Recent Replies
Comment: Filtering VCF files based on VAF giving incorrect results
by
Arton
• 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
Comment: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
Pierre Lindenbaum
161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 70
Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
▴ 10
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R
by
jared.andrews07
★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
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