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Genome reference fpr variant annotation of deleterious variants?
variants reference genome annotation deleterious functional prediction
4.3 years ago by ja569116 • 0
8
votes
11
replies
4.0k
views
directionality of RRBS
directional non-directional RRBS
updated 4.1 years ago by ★ 3.1k • written 4.3 years ago by ▴ 140
0
votes
3
replies
1.2k
views
Human Genome
GRCH37
updated 4.3 years ago by ▴ 360 • written 4.3 years ago by ▴ 20
7
votes
14
replies
5.3k
views
GTF file how do I search for duplicates of Gene ID and print them out
GTF Bash
updated 4.3 years ago by ★ 1.1k • written 4.3 years ago by ▴ 10
3
votes
2
replies
1.0k
views
Finding a Protein from Pepdites sequence
BLASTP
updated 4.3 years ago by ★ 30k • written 4.3 years ago by ▴ 10
7
votes
5
replies
2.3k
views
How can I extract protein sequence from gff file?
sequence bash gff
updated 4.3 years ago by ▴ 140 • written 4.3 years ago by ▴ 30
1
vote
6
replies
9.9k
views
GATK Input files reference and features have incompatible contigs: No overlapping contigs found.
reference gatk
4.1 years ago by Jordi ▴ 60
2
votes
2
replies
1.1k
views
Find the transcripts of genomic coordinates
Python
updated 4.3 years ago by ▴ 90 • written 4.3 years ago by • 0
0
votes
5
replies
1.4k
views
Looking for data
epistasis
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 10
0
votes
0
replies
519
views
Uneven numbers of phenotype and genotype
GenEpi
4.3 years ago by Mollie ▴ 10
2
votes
4
replies
1.5k
views
MagicBLAST only using one thread
MagicBLAST
updated 4.3 years ago by ▴ 160 • written 4.3 years ago by ▴ 80
0
votes
5
replies
1.2k
views
Converting plink to GenEpi files
plink GenEpi
updated 4.3 years ago by 2.9k • written 4.3 years ago by ▴ 10
11
votes
7
replies
15k
views
7 follow
Is there a way to download FASTq files from SRR IDs?
eutility fastq sra
updated 4.3 years ago by ▴ 90 • written 8.1 years ago by ▴ 80
5
votes
7
replies
5.7k
views
fastq-dump error
SRAToolkit fastq-dump
updated 2.2 years ago by 45k • written 4.3 years ago by • 0
3
votes
4
replies
1.5k
views
bowtie2 unaligned option not writing to file
bowtie2
updated 4.3 years ago by 11k • written 4.3 years ago by ▴ 80
0
votes
1
reply
703
views
interpretation of vcf calls
SNP
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
7
votes
12
replies
2.9k
views
7 follow
Why do I lose sequences when converting my bam files into fastq?
fastq bam bamToFastq
updated 4.3 years ago by 15k • written 4.3 years ago by ▴ 260
4
votes
2
replies
2.3k
views
Different peak sites from .xls and .narrowPeak, macs2 output
diffbind atac-seq macs2 chip-seq callpeak
4.3 years ago by sh.kazempour94 ▴ 20
2
votes
7
replies
3.4k
views
6 follow
Load GSEA software results into R
GSEA R plot
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 30
0
votes
0
replies
1.4k
views
Job: HIRING: Senior Software Developer- UC Santa Cruz Genomics Institute
software-developer bioinformatics-engineer genomics
updated 4.2 years ago by 45k • written 4.3 years ago by ▴ 30
0
votes
1
reply
2.3k
views
Biopython Align: making substitution matrix for global and local alignments
global local biopython
updated 4.3 years ago by 22k • written 4.3 years ago by ▴ 10
0
votes
0
replies
663
views
Job: HIRING: Sr Bioinformatician - UC Santa Cruz Genomics Institute
software-engineer pathogen genomics
updated 4.2 years ago by 45k • written 4.3 years ago by ▴ 30
0
votes
2
replies
2.5k
views
Conversion of SNP array data to PLINK format
SNP plink
updated 4.3 years ago by ▴ 20 • written 5.0 years ago by • 0
0
votes
1
reply
696
views
Strandedness of RNAseq data from SAM alignment flag
SAMflag Strandanalysis RNAseq
updated 4.3 years ago by 15k • written 4.3 years ago by • 0
0
votes
0
replies
842
views
COLOC.abf priors
COLOC
4.3 years ago by Filago ▴ 110
0
votes
2
replies
985
views
Ideas to represent RNA-seq expression profile (Z-scores) and the significance level at the same time
R RNAseq
updated 4.3 years ago by ★ 3.0k • written 4.3 years ago by ★ 1.5k
9
votes
13
replies
2.9k
views
mapped reads (m aligned) is higher for a subset sample?
salmon fastqc multiqc RNA-seq
updated 4.3 years ago by 89k • written 4.3 years ago by ★ 1.1k
0
votes
1
reply
1.2k
views
How to find coefficients of all genes for prediction of risk score with some threshold using multivariate cox regression model in TCGA-LIHC dataset ?
cox risk-score survival-analysis TCGA
written 4.3 years ago by • 0
0
votes
0
replies
744
views
Analysis of CRISPR screening with very strong positive selection
MAGeCK CRISPR
4.3 years ago by di4mond • 0
0
votes
1
reply
1.6k
views
Build phylogenetic tree with alignment file
nwk phylogenetic aln alignment
updated 4.3 years ago by 56k • written 4.3 years ago by ▴ 70
0
votes
0
replies
1.1k
views
Job: PhD scholarship in bioinformatics in Rostock (Baltic Coast), Germany
aging nutrition
updated 4.2 years ago by 45k • written 4.3 years ago by • 0
0
votes
1
reply
1.2k
views
How do I correctly add a plasmid sequence with multiple genes to a gtf as well as fasta file?
gtf fasta plasmid
updated 4.3 years ago by ▴ 160 • written 4.3 years ago by • 0
7
votes
4
replies
2.1k
views
Up to date bulk RNA-seq Quality Control tools?
QC RNA-seq
4.3 years ago by Pratik ★ 1.1k
0
votes
4
replies
1.3k
views
AWS EC2 connection with External hard drive (portable hard drive)
EC2 AWS
updated 4.2 years ago by 45k • written 4.3 years ago by • 0
0
votes
1
reply
1.1k
views
samtools mpileup: error CRC32 failure
sequencing SNP genome next-gen gene
updated 4.3 years ago by 166k • written 4.3 years ago by ▴ 10
1
vote
1
reply
783
views
Finding if genes present in a gene list intersect genomic intervals
bed encode gene
3.9 years ago by alexmondaini ▴ 20
0
votes
1
reply
2.1k
views
Packages installation: Permission denied
bioconductor R packages
updated 4.3 years ago by 12k • written 4.3 years ago by ▴ 10
1
vote
2
replies
888
views
Split a sam file by chromosome
CNVs NGS PRISM
updated 4.3 years ago by 153k • written 4.3 years ago by ▴ 20
4
votes
6
replies
2.8k
views
Trim bam file reads to the same length
RNA-Seq genome sequencing next-gen
updated 4.3 years ago by 9.3k • written 5.6 years ago by ▴ 40
0
votes
0
replies
768
views
Job: Postdoc position on Modeling Gene Disruptions involved in Speech and Language Impairment in Human Neurons
transcriptomics single epigenetics cell
4.3 years ago by pancakeplant ▴ 10
1
vote
2
replies
2.6k
views
Salmon quant produced an error
Salmon Linux
updated 20 months ago by ▴ 10 • written 4.3 years ago by ▴ 30
2
votes
1
reply
1.0k
views
effects of posttranslational protein modifications database?
post-translational-modification protein
updated 13 months ago by 45k • written 4.3 years ago by ▴ 30
0
votes
1
reply
1.6k
views
bcftools add AD column
ad bcftools vcf
updated 4.3 years ago by 12k • written 4.3 years ago by • 0
1
vote
5
replies
2.4k
views
Trimmomatic: Unknown trimmer error
fastq trimmomatic RNA-seq
4.3 years ago by foxiw ▴ 10
0
votes
0
replies
1.6k
views
Job: Research Assistant in the Systems Environmental Microbiology Group at DTU Biosustain
engineering Strain
4.3 years ago by info ▴ 80
1
vote
1
reply
926
views
CNV in EPIC Illumina DNA methylation
bed CNV Conumee
updated 2.5 years ago by 45k • written 4.3 years ago by • 0
4
votes
4
replies
2.6k
views
awk, count and print the number of lines following a separator then add value of header to that column
awk
updated 4.3 years ago by 12k • written 4.3 years ago by ▴ 20
1
vote
2
replies
1.6k
views
FastQC report of the metagenomic data
Metagenomics Microbiome WholeShotgunMetagenome FastQC Data-Analysis
4.3 years ago by serene.s • 0
0
votes
1
reply
928
views
copy number variation and aneuploidy
aneuploidy number copy variation
updated 4.3 years ago by ★ 3.0k • written 4.3 years ago by • 0
0
votes
4
replies
1.7k
views
Getting biological replicates from SRA run NCBI
fastq AWS SRA RNAseq
17 months ago by Andres ▴ 20
121,903 results • Page 633 of 2439
Recent Votes
Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Recent Replies
Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
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