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1,000 results • Page 6 of 20
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9
votes
12
replies
7.3k
views
How to align reads on reference using python?
genome sequence gene sequencing
updated 5.4 years ago by 47k • written 5.4 years ago by ▴ 10
10
votes
5
replies
7.3k
views
how to remove asterisk characters from a translated sequences (fasta format)?
sequencing Assembly alignment
updated 21 months ago by 43k • written 8.7 years ago by ★ 1.9k
4
votes
5
replies
7.3k
views
How to convert txt or csv files into ped files?
plink ped R python
updated 5.6 years ago by 11k • written 5.8 years ago by ▴ 10
15
votes
11
replies
7.3k
views
Filtering rRNA contamination (indicated by GC content plots) from RNA-seq data
RNA-Seq QC
5.5 years ago by jackgrayner ▴ 100
4
votes
8
replies
7.3k
views
SRA submission Error
SRA
5.4 years ago by suren04 ▴ 20
3
votes
4
replies
7.3k
views
Trimmomatic not removing all Nextera adapters or N base calls
trimming nextera trimmomatic
updated 8.0 years ago by 20 • written 8.0 years ago by ★ 3.4k
13
votes
16
replies
7.3k
views
6 follow
Confused about how to generate a consensus sequence after bwa
bwa samtools mpileup
5.4 years ago by DNAngel ▴ 250
4
votes
11
replies
7.3k
views
demultiplexing with fastq having barcode and primer sequence
sequencing next-gen demultiplex
7.6 years ago by tonja.r ▴ 600
3
votes
8
replies
7.3k
views
read trimming for small RNA NGS data
RNA-Seq miRNA read trimming Trimmomatic
7.8 years ago by ron128 ▴ 10
2
votes
8
replies
7.3k
views
BWA mem failing to locate index files
bwa index
4.8 years ago by aalith ▴ 20
0
votes
6
replies
7.3k
views
T-Statistic Stochastic Neighbour Embedding In R For Grouping Gene Expression Data
r gene-expression
11.9 years ago by Diana ▴ 910
5
votes
5
replies
7.3k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 4 weeks ago by • 0 • written 3.8 years ago by ★ 1.8k
1
vote
6
replies
7.3k
views
using bcftools/samtools to generate consensus using reference + variants; output is a truncated reference
samtools bcftools mosaik consensus rc454
updated 24 months ago by 43k • written 9.2 years ago by ▴ 10
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
0
votes
7
replies
7.3k
views
Problem in in alignment by muscle
sequence muscle alignment
updated 10 months ago by 43k • written 6.8 years ago by ▴ 70
0
votes
5
replies
7.2k
views
STAR alignment, RNA-seq
RNA-Seq
7.1 years ago by prasoonagar ▴ 10
0
votes
10
replies
7.2k
views
Limma Analysis, BH Correction - adj. P-value all the same value
R limma
8.2 years ago by Cale Reid • 0
7
votes
15
replies
7.2k
views
6 follow
blastn error - NCBI C++ Exception
assembly blast alignment
updated 2.1 years ago by 15k • written 3.1 years ago by ▴ 980
4
votes
8
replies
7.2k
views
Error while demultipleaxing .bcl to .fastq files
sequencing genome alignment
updated 20 months ago by 43k • written 8.7 years ago by ▴ 220
1
vote
3
replies
7.2k
views
TCONS lincRNA ID to ensembl gene ID conversion
lincRNA TCONS id
7.6 years ago by WMJ ▴ 10
9
votes
3
replies
7.2k
views
Statistical Distributions In Rna-Seq Data Analysis
statistics rna
updated 5.2 years ago by 20 • written 12.1 years ago by ▴ 380
2
votes
4
replies
7.2k
views
how can I make input file for Haploview from Output files of inferred haplotypes by fastPHASE?
Haploview phased-haplotypes fastPHASE
updated 2.5 years ago by 43k • written 9.9 years ago by ▴ 210
5
votes
14
replies
7.2k
views
Duplicate/identical reads in fastq file
sequencing fastq
5.4 years ago by cpad0112 21k
2
votes
5
replies
7.2k
views
bwa sampe error [fread] Unexpected end of file
bwa software error
updated 8.1 years ago by 142k • written 8.1 years ago by ▴ 20
3
votes
9
replies
7.2k
views
convert blastn output file to sam/bam
blast blast2sam blast2bam
8.8 years ago by federica.r299 • 0
3
votes
4
replies
7.2k
views
Effective Population Size (Ne) From Nucleotide Diversity (Pi) And Mutation Rate (Mu)
population mutation nucleotide
11.8 years ago by Stingery ▴ 20
0
votes
0
replies
7.2k
views
Error in grid.Call.graphics(L_setviewport, vp, TRUE) : non-finite location and/or size for viewport
gviz
updated 22 months ago by 43k • written 8.7 years ago by ▴ 10
1
vote
7
replies
7.1k
views
How to convert gtf to bed format
gtf bed
6.4 years ago by Vasu ▴ 770
0
votes
2
replies
7.1k
views
R script - Error: protect(): protection stack overflow
tsne pca r bigdata
6.9 years ago by Chen Mor • 0
1
vote
3
replies
7.1k
views
Half missing genotype in *.ped files
genome next-gen sequencing plink pedfiles
5.2 years ago by 123sanjanagupta ▴ 10
4
votes
8
replies
7.1k
views
Z-Score On Raw Counts
rnaseq
11.1 years ago by camelbbs ▴ 710
1
vote
19
replies
7.1k
views
Conda install package - different internals
R software error
updated 4.8 years ago by 20 • written 4.8 years ago by ▴ 30
0
votes
4
replies
7.1k
views
Mauvealigner Error
updated 8.2 years ago by 20 • written 10.9 years ago by ★ 1.2k
1
vote
6
replies
7.1k
views
Multiple START codons in DNA/RNA Translation
Translation RNA DNA Codons
updated 4.0 years ago by 20 • written 4.1 years ago by ▴ 20
1
vote
16
replies
7.1k
views
After sorting bam file not able to index ?
alignment next-gen
updated 5.2 years ago by 20 • written 5.4 years ago by ▴ 980
7
votes
19
replies
7.1k
views
[R] Microarray analysis interpreting logFC after makeContrasts
microarray R
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 10
2
votes
9
replies
7.1k
views
Requirements for running HISAT2
ngs RNA-Seq hisat indexing
6.5 years ago by Arindam Ghosh ▴ 510
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 43k • written 9.3 years ago by ▴ 270
0
votes
1
reply
7.1k
views
How To Run The Modeller From The Command Line Rather Than A Gui
modeling
updated 11.4 years ago by ★ 2.5k • written 11.4 years ago by ▴ 70
5
votes
11
replies
7.0k
views
Error while running miso
RNA-Seq splicing
updated 21 months ago by 43k • written 8.8 years ago by ▴ 40
7
votes
4
replies
7.0k
views
Which genome files to use for STAR?
alignment star genome
5.0 years ago by Nico80 ▴ 80
1
vote
5
replies
7.0k
views
Java Error "Concurrent.Executionexception" While Running Trimmomatic V0.32
java qualitycontrol
updated 2.4 years ago by 43k • written 10.3 years ago by ★ 1.8k
1
vote
7
replies
7.0k
views
samtools mpileup error
Assembly software error next-gen sequence
updated 2.5 years ago by • 0 • written 6.6 years ago by • 0
2
votes
3
replies
7.0k
views
How to convert RDS file into excel
Python R data
updated 2.0 years ago by 11k • written 2.0 years ago by • 0
2
votes
5
replies
7.0k
views
Tophat Protocol Error Occured At Step 4
tophat rna-seq
updated 24 months ago by 43k • written 12.0 years ago by ▴ 110
1
vote
4
replies
7.0k
views
Unsupervised Hierarchical Cluster Heatmap
R Heatmap ggplot2
updated 6.3 years ago by 20 • written 6.3 years ago by ▴ 30
1
vote
1
reply
7.0k
views
MACS2 Narrow peak (narrowPeak) output format
macs2 ChIP-Seq
updated 7.3 years ago by 20 • written 7.3 years ago by ▴ 260
0
votes
3
replies
7.0k
views
How to convert txt file to ped and map using plink
plink ped map txt
7.4 years ago by BlackHole • 0
0
votes
2
replies
7.0k
views
Illumina adapter diagram
illumina sequencing adapter-trimming
updated 22 months ago by 43k • written 9.1 years ago by • 0
7
votes
1
reply
7.0k
views
createRepeatLandscape in RepeatMasker
RepeatMasker
7.7 years ago by a.rex ▴ 350
1,000 results • Page 6 of 20
Recent Votes
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
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
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Recent Replies
Comment: Doubt about the process of annotation, detection, identification and classificat by MarcosCosta • 0
Thank you very much, you've helped me a lot
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…
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