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1,000 results • Page 2 of 20
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1
vote
12
replies
3.4k
views
Can anyone explain the weird Insert Size HIstogram
RNA-Seq alignment sequencing
updated 22 days ago by 68k • written 5.3 years ago by ▴ 170
1
vote
12
replies
619
views
weird alignment results for RNAseq data
hisat2 star
updated 9 months ago by 21k • written 9 months ago by ▴ 220
3
votes
12
replies
3.5k
views
Chromosome Data -- Only genes for given chromosome, without introns and with annotated motifs, possible?
Assembly gene sequence genome rna-seq
updated 10 months ago by 37k • written 8.1 years ago by ▴ 80
2
votes
12
replies
1.7k
views
Nothing will align with HTSeq?
RNA-Seq htseq
updated 4 months ago by 37k • written 7.4 years ago by ▴ 610
0
votes
12
replies
795
views
Can't exec "cd": No such file or directory at ./PAst.pl line 43
PAst
updated 9 months ago by 14k • written 9 months ago by ▴ 10
0
votes
12
replies
743
views
Splitting CRAM files
CRAM-files sequence-alignment
7 weeks ago by langziv ▴ 20
2
votes
12
replies
496
views
how to align an intron from a complex
genomic
updated 7 months ago by 47k • written 7 months ago by • 0
2
votes
12
replies
1.0k
views
The best way to get gene lengths for 15K+ genes?
r EDAseq RNA-seq
4 months ago by JACKY ▴ 70
4
votes
12
replies
830
views
Bulk RNA seq: all p adjusted are the same
p-adj RNA-seq differential-gene-expression
updated 5 weeks ago by 37k • written 8 months ago by ▴ 10
0
votes
12
replies
2.5k
views
Allpaths- Keep getting ConvertToFastbQualb.pl failed for group 'paired_ends' when I run PrepareAllPaths
next-gen Assembly
updated 5 weeks ago by 37k • written 7.6 years ago by ▴ 80
0
votes
12
replies
3.7k
views
miRDeep2: expression reads and input reads not tallying
miRDeep2 miRNA
updated 12 months ago by 37k • written 8.2 years ago by ▴ 40
0
votes
12
replies
1.8k
views
Tax4Fun2 - error
tax4fun silva blast
updated 5 months ago by 125k • written 11 months ago by ▴ 10
1
vote
12
replies
3.1k
views
How to run multiple alignment and SNP-calling of WGS data in .gb and .fasta using Python or Ruby/Java or any free software?
alignment sequencing software
updated 7 months ago by 37k • written 7.8 years ago by ▴ 60
0
votes
11
replies
2.2k
views
mpiBLAST Score and E-value Calculation
blast sequence
updated 8 months ago by 37k • written 7.9 years ago by • 0
4
votes
11
replies
2.2k
views
7 follow
Getting coding sequence length
NCBI Gene CDS
updated 7 months ago by ▴ 350 • written 2.5 years ago by ★ 4.1k
1
vote
11
replies
3.8k
views
Pileup viewer for VCF v4.2
bcftools-merge vcf vcf4.2 IGV
updated 11 months ago by 37k • written 8.2 years ago by ★ 3.1k
3
votes
11
replies
12k
views
What is the acceptable % of reads that map to no feature (in RNASeq)?
htseq RNA-Seq STAR
updated 9 months ago by 37k • written 8.0 years ago by ▴ 120
0
votes
11
replies
732
views
Python - Samtools mpileup find snps with allele frequency
snp mpileup python samtools
7 months ago by pablosolar.r ▴ 20
0
votes
11
replies
1.3k
views
Bowtie2 no build the index
bowtie2
updated 12 months ago by 8.3k • written 12 months ago by • 0
5
votes
11
replies
1.0k
views
Differences in unique mapping between STAR and BLAST?
alignment RNAseq BLAST STAR
12 months ago by steel1990 ▴ 20
1
vote
11
replies
2.6k
views
merge samples in phyloseq returns NAs
R phyloseq biom
updated 12 weeks ago by • 0 • written 2.5 years ago by ▴ 10
2
votes
11
replies
2.0k
views
bbmap.sh: line 352 /random number/ Killed
bbmap bbmap.sh: line 352 Killed metagenome
updated 11 months ago by 125k • written 2.9 years ago by • 0
3
votes
11
replies
736
views
RepeatMasker error
repeatmasking transciptome RNA-seq
updated 6 months ago by ★ 1.8k • written 6 months ago by ▴ 100
4
votes
11
replies
5.0k
views
Correct way to calculate VAF (Variant allele fraction) from a VCF file
VCF snp
5 months ago by prasundutta87 ▴ 640
10
votes
11
replies
8.1k
views
How to adjust my manhattan plot to look better?
qqman manhattan R
updated 8 months ago by 37k • written 7.8 years ago by ▴ 40
1
vote
11
replies
3.9k
views
Running survival analysis using Rplink
Cox Survival R GWAS PLINK
updated 10 months ago by 37k • written 8.0 years ago by ▴ 40
8
votes
11
replies
1.1k
views
using STAR instead of HISAT2
STAR
updated 6 months ago by 37k • written 6 months ago by ▴ 60
3
votes
11
replies
898
views
Feature count is very low using htseq-count
htseq bbmap
10 months ago by salmon ▴ 10
5
votes
11
replies
6.2k
views
Error while running miso
RNA-Seq splicing
updated 6 months ago by 37k • written 7.5 years ago by ▴ 40
0
votes
11
replies
1.1k
views
Error in Importing data in qiime2
Metagenomics Sequencing Qiime2 Amplicon
6 months ago by Vaishnavi • 0
2
votes
11
replies
1.2k
views
how to run seqkit in a loop with multiple files
seqkit scaffolds python
11 months ago by Kumar ▴ 150
3
votes
11
replies
4.7k
views
BWA error: no ID within the read group line
bwa readgroups RG parallel
updated 11 months ago by 37k • written 2.1 years ago by ▴ 50
4
votes
11
replies
958
views
Running STAR
STAR
5 months ago by Chris ▴ 60
0
votes
11
replies
493
views
Problem with Trimmomatic Multiple Paired-End sequencing.
Trimmomatic
updated 9 days ago by 125k • written 11 days ago by • 0
3
votes
10
replies
3.1k
views
Somaticsniper Hangs Up
updated 9 months ago by 37k • written 8.9 years ago by ▴ 80
7
votes
10
replies
3.3k
views
Choosing phylogenetic approaches
phylogeny
updated 11 months ago by 37k • written 8.4 years ago by ▴ 100
4
votes
10
replies
2.2k
views
downloading and running tidyverse package in R
seq analysis tidyverse rna
6 months ago by bioinformatics ▴ 10
5
votes
10
replies
4.4k
views
Antisense transcription - how to detect it?
RNA-Seq antisense
updated 5 months ago by 37k • written 7.3 years ago by 13k
2
votes
10
replies
980
views
Generate pin phr and psq files of a fasta file
openms proteomics knime fasta uniprot
updated 9 months ago by 14k • written 10 months ago by ▴ 40
1
vote
10
replies
3.1k
views
R code to match the positions for repetitive elements in rmsk file for mouse mm10 with mouse genome
next-gen R RNA-Seq
updated 9 months ago by 37k • written 7.9 years ago by ▴ 590
4
votes
10
replies
3.5k
views
TCGA normalized count data of 1000 samples for DGE
RNA-Seq TCGA
updated 4 days ago by 37k • written 7.7 years ago by ▴ 460
2
votes
10
replies
546
views
Can I directly compare the regions defined by peaks from pair-end 50 and pair-end 100 ATAC-seq?
ATAC-seq
updated 4 months ago by 68k • written 4 months ago by ▴ 60
7
votes
10
replies
3.7k
views
PSMC using haploid genomes
haploid genome PSMC
updated 10 months ago by 37k • written 8.2 years ago by ▴ 200
0
votes
10
replies
872
views
DeSeq2 "some values in assay are negative"
RNAseq
11 weeks ago by Morris_Chair ▴ 330
0
votes
10
replies
701
views
using txt file to pass pathways for pipelines
muscle seqkit bash fasta
updated 6 months ago by 37k • written 6 months ago by • 0
1
vote
10
replies
969
views
Weird results for scRNA-seq
scRNA-seq GEO
updated 4 weeks ago by ▴ 60 • written 6 weeks ago by ▴ 100
5
votes
10
replies
4.0k
views
alignment rate in bowtie2
sequencing RNA-Seq
updated 8 months ago by 37k • written 7.0 years ago by ★ 4.1k
6
votes
10
replies
750
views
Understanding bam tracks
RNA sequencing bam
updated 4 months ago by 152k • written 4 months ago by ▴ 30
5
votes
10
replies
545
views
How to change chromosome names in assembly fasta downloaded from NCBI?
grch38 ncbi grch37 fasta
4 months ago by magnolia ▴ 20
6
votes
10
replies
3.1k
views
Problem with logFC values
EdgeR logFC next-gen R RNA-Seq
updated 11 months ago by 37k • written 8.2 years ago by • 0
1,000 results • Page 2 of 20
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Answer: how to do a reliable single cell sequencing analysis? by ATpoint 68k
The usual approach for starters would be to follow guided and well-accepted tutorials. That would (incomplete list) be: - The Biocon…
Answer: a problem with getBM by sanaz • 0
head(ensembl_ids) X baseMean log2FoldChange lfcSE stat pvalue padj 1 ENSG00000000938.13 1344.2587 2.107…
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Hello and Thanks! OK, I should have written "The gene lists I have prepared" instead of "The DEG lists I have prepared". In any case, is …
Comment: a problem with getBM by Mike Smith ★ 1.9k
Can you update your post to show some examples of what's in your `ensembl_ids` object? Perhaps the contents of `head(ensembl_ids)`. It's …
Answer: trainGlimmerHMM Error while training a genome by congliu37 • 0
Hello, I got the same error using ~20,000 genes for training and it was solved by reducing training gene set. I assume GlimmerHMM was no…
Comment: How to Calulate Allele Frequency from a VCF File? by Jeremy Leipzig 21k
That's correct. You don't have biallelic alleles in mitochondria, so you can use either the Allele depth (AD) or depth of coverage (DP) for…
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I just published a [post][1] on my blog, in which I include a simple R function for computing TMB. Try to see if that helps. I followed the…
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Thank you FrankStarling, ATpoint, jv, these were so helpful.
Comment: translate CDS to prot formatted with nt nubers by Pierre Lindenbaum 152k
> with nucleotide numbers and DNA/prot aligned line by line what does it mean ? Create a Minimal, Reproducible Example to enable others t…
Comment: How to translate CDS to an amino acid sequence by vvasta • 0
I tried several of the online DNA translation tools but have not found one that would output DNA/prot alignment with nucleotide number w…
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
but you already knew it. https://www.biostars.org/p/9551097/#9551098
Comment: How possible deadlocks are there while migrating from MYISAM to InnoDb? by Pierre Lindenbaum 152k
your question is not related to bioinformatics. Ask stackoverflow.com.
Comment: Statistical test for checking cis regulation? by Fabio Marroni ★ 2.9k
Hi lumos. It is not very clear to me what kind of information are you using for the test and how are you measuring cis-regulation. Are you …
Comment: Error 134 while aligning using hisat2 by Fabio Marroni ★ 2.9k
Other instances of the same error were indeed related to disk [space][1]. Can you post the output of the command: `df -h /bams/`? Another p…
Comment: **Error: unable to open file or unable to determine types for file** by Pierre Lindenbaum 152k
``` Please ensure that your file is TAB delimited (e.g., cat -t FILE). - Also ensure that your file has integer chromosome coordinates in t…
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