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News: :: FINAL CALL :: Online Course - A Practical Introduction to NGS Data Analysis (April 28 - 30, 2021)
NGS DNA-Seq Workshop Mapping RNA-Seq
4.5 years ago by David Langenberger 11k
0
votes
0
replies
1.4k
views
Problems running strelka2
variant calling ngs strelka
4.5 years ago by arne.zibat • 0
0
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0
replies
959
views
Pymol to visualize MSA conservation
alignment sequence msa
4.5 years ago by katamaneni.akhila • 0
1
vote
0
replies
586
views
The problems of make_html.pl when install the miRDeep2
RNA-Seq
updated 4.5 years ago by 35k • written 4.5 years ago by ▴ 20
0
votes
0
replies
646
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Question about a paper called Reference flow: reducing reference bias using multiple population genomes
RNA-Seq sequence
4.5 years ago by minghuiguo448 • 0
0
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0
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1.3k
views
Should I calculate beta diversity with or without rarefaction?
diversity R
4.5 years ago by dpc ▴ 250
0
votes
1
reply
2.2k
views
Generate consensus from contig alignment to reference sequence
Assembly alignment
4.5 years ago by daewowo ▴ 80
3
votes
1
reply
1.3k
views
What should be the value of Sjdboverhang in STAR?
STAR index reference sjdbOverhang
4.5 years ago by DareDevil ★ 4.4k
16
votes
13
replies
16k
views
Bash scripting FastQC for multiple fastq files in multiple directories
RNA-Seq bash fastQC
updated 4.5 years ago by ★ 4.4k • written 6.9 years ago by ▴ 20
0
votes
0
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1.2k
views
How maftools oncoplot deal with Splice_Site mutation
maftools oncoplot SNV Splicing
4.5 years ago by lincaijin1994 ▴ 50
1
vote
3
replies
1.2k
views
The problems when i install the miRDeep2
RNA-Seq
4.5 years ago by 51203903042 ▴ 20
0
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5
replies
1.1k
views
The problems when i map to genome by mapper.pl in miRDeep2
RNA-Seq
4.5 years ago by 51203903042 ▴ 20
4
votes
7
replies
1.6k
views
not able to run Deseq 2
RNA-Seq alignment sequence assembly
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
2
votes
4
replies
1.4k
views
Gene annotations of mammalian genomes
Gene annotation mammalian genomes
4.5 years ago by arsala521 ▴ 60
0
votes
0
replies
1.3k
views
Deletions are missed from consensus sequence even when they are predominant. Is this common to vcf2fq of vcfutils?
vcf2fq consensus bcftools indel
4.5 years ago by malaya77 • 0
2
votes
0
replies
1.1k
views
Tool: New location tracking tool for SARS-CoV-2 variant surveillance
sars-cov-2 variant covid-19
updated 2.3 years ago by 45k • written 4.5 years ago by ▴ 100
3
votes
3
replies
4.7k
views
Playing With Mysql/Ensembl (I): Mapping 'Gene' To 'Xref'
ensembl mysql
updated 22 months ago by 45k • written 15.5 years ago by 166k
1
vote
2
replies
1.0k
views
Seeking for siRNA screeing data analysis
R siRNA gene Statistic
4.5 years ago by podderbiswajit4 • 0
8
votes
1
reply
1.9k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 2.5 years ago by 45k • written 4.5 years ago by 89k
3
votes
5
replies
1.2k
views
conceptual question about paired end sequencing
sequencing illumina
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 420
3
votes
5
replies
4.8k
views
Cellranger count command for single end fastq
RNA-Seq sequencing
updated 2.6 years ago by 45k • written 4.8 years ago by ▴ 70
1
vote
1
reply
668
views
How to generate simulated RNA-seq data
RNA-Seq
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
0
votes
0
replies
1.5k
views
germline vs somatic CNV GATK calling
CNV germline somatic GATK WGS
4.5 years ago by cocchi.e89 ▴ 290
0
votes
0
replies
625
views
KEGG mapping of Go ids
RNA-Seq
4.5 years ago by aranyak111 • 0
24
votes
10
replies
9.5k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 2.5 years ago by 45k • written 5.1 years ago by 13k
0
votes
1
reply
3.0k
views
findOverlapsOfPeaks() of package ChIPpeakAnno in R
R
updated 4.5 years ago by ▴ 10 • written 8.5 years ago by ▴ 550
0
votes
1
reply
2.8k
views
No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package
ChIP-Seq annotation
updated 3.1 years ago by 45k • written 10.0 years ago by ▴ 10
0
votes
7
replies
3.2k
views
Cholmod error when using decontX package
R RNA-Seq sequencing
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 30
2
votes
8
replies
1.6k
views
status check missing from multiQC report
RNA-Seq fastqc
4.5 years ago by Lauren • 0
0
votes
0
replies
1.8k
views
Job: Research Associate / Sr. Research Associate
Research
updated 2.2 years ago by 45k • written 4.5 years ago by ▴ 70
2
votes
2
replies
1.9k
views
Difference between read depth, allelic depth and bam readcounts
bam vcf sequencing genotype
updated 4.5 years ago by ▴ 10 • written 4.5 years ago by ▴ 50
1
vote
1
reply
752
views
Summarizing list of Genbank Assembly Accessions
assembly gene genome alignment
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
0
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1
reply
4.9k
views
SNPs density ( count/ per Kb) calculation from VCF file
SNP SNPs density Count/Kb
updated 4.5 years ago by ▴ 10 • written 4.9 years ago by ▴ 220
0
votes
1
reply
1.1k
views
How do I compare two similar PPI networks using Cytoscape?
cytoscape STRING PPI networks
updated 4.5 years ago by ▴ 650 • written 4.5 years ago by ▴ 20
0
votes
0
replies
893
views
Job: Postdoc in Genetic/Epigenetic/Observational Epidemiology (Mount Sinai, NY)
epidemiology genetics neurodevelopment epigenetics
updated 2.2 years ago by 45k • written 4.5 years ago by • 0
1
vote
1
reply
975
views
CWL input files as secondaryFiles JS
CWL input secondaryFiles
updated 4.2 years ago by ★ 1.9k • written 4.5 years ago by ▴ 290
1
vote
3
replies
1.8k
views
different read names in paired-end data
fastq file read name header ABI-Solid
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 270
0
votes
0
replies
718
views
Reference files that can be used for mapping ERVs?
alignment
4.5 years ago by tesic93 ▴ 40
5
votes
4
replies
5.1k
views
6 follow
Gene correlation with single cell data?
RNA-Seq gene
updated 21 months ago by ▴ 10 • written 4.5 years ago by ▴ 50
3
votes
3
replies
2.9k
views
Effect of removing secondary/supplementary alignments from BAM file?
ngs covid-19 SNP
4.5 years ago by cg1440 ▴ 60
12
votes
2
replies
1.8k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 2.5 years ago by 45k • written 4.5 years ago by 13k
0
votes
5
replies
2.4k
views
bam2cfg.pl not able to find statistics : Breakdancer
gen Assembly software error
updated 4.5 years ago by 20 • written 7.0 years ago by ▴ 1000
3
votes
5
replies
4.3k
views
PLINK:Error: Variant '.' is not biallelic. To obtain a full list of merge failures
SNP Assembly genome next-gen
4.5 years ago by williamsbrian5064 ▴ 540
0
votes
0
replies
775
views
Is it possible to impute missing phenotypes (case/control) in Plink .fam files in a GWAS study?
illumina plink GWAS IDAT
4.5 years ago by doughan.albert • 0
0
votes
3
replies
2.0k
views
Uploading text file or any file format in Flexdashboad
R
4.5 years ago by majeedmj.ict ▴ 20
0
votes
0
replies
833
views
How to create link file from NUCmer output
nucmer
4.5 years ago by agata88 ▴ 870
0
votes
1
reply
772
views
How can I convert mouse microarray's Probe IDs into gene names?
R next-gen gene
4.5 years ago by moutazhatem.mh • 0
1
vote
2
replies
897
views
merge paired-end sequencing
SNP merge gatk
4.5 years ago by gubrins ▴ 350
0
votes
4
replies
960
views
Error when running Rscript under Ubuntu
R
4.5 years ago by Evy_00 • 0
2
votes
3
replies
1.4k
views
extract region.txt from bam file
alignment Assembly rna-seq
4.5 years ago by madiha_shabbir46 ▴ 10
121,908 results • Page 691 of 2439
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Tried building a compact sequence format with 4-bit storage
Comment: Tried building a compact sequence format with 4-bit storage
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
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Recent Replies
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
No overlapping reads? Have you checked for contamination?
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
I see, but the reason I was planning on using a 4bit system is so that there wouldn't be too much data loss but thank you for the suggesti…
Comment: Splice junctions plots for long-read seq data by alison.ludzki • 0
Thank you! I will check out miso!
Comment: Hifiasm is getting killed while trying to assemble a genome by pranavdatar01 • 0
I did subsample the data to 30x coverage. I did run hifiasm on it, the log file did show some contents, but hifiasm ended again, stating th…
Comment: Tried building a compact sequence format with 4-bit storage by Alex Reynolds 36k
Using four bits for storage won't beat 2bit, of course, but direct access to a sequence of interest sounds interesting and useful and might…
Comment: Hifiasm is getting killed while trying to assemble a genome by Panos ★ 1.8k
Why don't you subsample your HiFi reads and try running hifiasm again? Maybe this will help if you have memory problems. However, I haven't…
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.
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