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121,907 results • Page 685 of 2439
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3
votes
5
replies
5.1k
views
Could somebody suggest free pathway visualization tool for omics data from plants?
Vizualization Pathways RNA-Seq
updated 4.5 years ago by ▴ 440 • written 7.3 years ago by ▴ 340
0
votes
2
replies
1.4k
views
Analysis of the gene set enrichment in clusters
biopython Fishertest genesetenrichment
4.5 years ago by stgr1202 • 0
0
votes
4
replies
1.7k
views
Puzzling Bowtie2 Input Error -S flag
bash bowtie2 alignment shell
4.5 years ago by geneticatt ▴ 140
0
votes
0
replies
806
views
Job: Postdoc openings @ NYC: Epigenetics / Long Reads / Microbiome
sequencing RNAseq microbiome methylation
4.5 years ago by fanggang ▴ 120
0
votes
0
replies
1.1k
views
Definition of soft threshold power with wgcna: SFT.R.sq vs truncated.R.sq columns
wgcna SFT
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
412
views
DNAzymes
sequencing
4.5 years ago by maryamtashakori96 • 0
3
votes
4
replies
3.4k
views
Excluding variants with a "LowQual" filter in bcftools consensus
snp bcftools covid-19 ngs
4.5 years ago by cg1440 ▴ 60
7
votes
9
replies
3.6k
views
Choosing a single consensus promoter/transcript for each gene (Mouse)
annotation ucsc general
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 70
1
vote
5
replies
4.4k
views
Issue about "Augustus did not recognize any genes"
Augustus BUSCO
4.5 years ago by boymin2020 ▴ 80
10
votes
10
replies
4.2k
views
7 follow
Pipeline transposable elements
transposon
updated 4.5 years ago by 15k • written 6.4 years ago by ▴ 50
1
vote
1
reply
1.3k
views
Gene sequences for a cell line
genome sequence
updated 4.5 years ago by ▴ 140 • written 4.7 years ago by ▴ 10
0
votes
0
replies
799
views
Stringtie output shows no expression for reference genes
stringtie programming annotation transcriptome rna
4.5 years ago by samhairle ▴ 20
5
votes
1
reply
992
views
How to evaluate phylogenetic congruence between two phylogenetic tree?
snp python perl genomics phylogeny
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 120
8
votes
16
replies
5.9k
views
bedtools bamtofastq generates fastq which cannot be gzip correctly?
gzip miseq bedtools fastq bamtofastq
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 90
3
votes
4
replies
2.4k
views
SARS-Cov-2 variant calling
sequencing variants sars-cov-2
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 130
6
votes
2
replies
5.0k
views
Understanding Seurat Object
RNA-Seq singlecell Seurat
4.5 years ago by patelk26 ▴ 340
1
vote
2
replies
1.2k
views
Is it possible to compare the expression of 2 genes based on count data?
counts RNA-Seq
4.5 years ago by Francois Piumi ▴ 70
14
votes
3
replies
2.5k
views
Is there any gene nomenclature conversion tool that recognizes old names?
genomics R annotation
updated 4.5 years ago by ▴ 340 • written 4.5 years ago by ▴ 70
0
votes
1
reply
1.2k
views
Scoring Metric Gene Clusters (General Inquiry)
genome matrix cluster antismash
updated 4.5 years ago by ▴ 140 • written 5.5 years ago by ▴ 80
4
votes
5
replies
3.6k
views
How to download entire human protein sequences from RefSeq database hrough command line?
Refseq programming
updated 4.5 years ago by ★ 3.9k • written 4.5 years ago by ▴ 80
0
votes
1
reply
805
views
Inclusivity Analysis SARS-CoV2
SARS-CoV-2
updated 20 months ago by 45k • written 4.5 years ago by • 0
3
votes
7
replies
4.1k
views
How to calculate frequencies of SNPs with respect to a particular allele by plink?
frequency snp plink
4.5 years ago by jamespower ▴ 100
0
votes
0
replies
1.5k
views
Job: Staff Data Scientist / Bioinformatician in Proteomics at Max Perutz Labs Vienna
proteomics massspectrometry
4.5 years ago by Markus • 0
0
votes
11
replies
2.9k
views
bbmap for FAIRE-seq and other line than reference
aligner mapping sequencing
4.5 years ago by boczniak767 ▴ 880
0
votes
1
reply
1.5k
views
What does the -0 flag of samtools fastq mean?
samtools
updated 4.5 years ago by ▴ 390 • written 4.5 years ago by ▴ 750
2
votes
4
replies
1.5k
views
How to grep every row for the every value of a column?
RGeneID
4.5 years ago by markgodek ▴ 50
1
vote
0
replies
1.4k
views
Analysing chromHMM output to get the correlation of binding patterns of interrogated DNA binding factors
pipeline general
4.5 years ago by munaj86 ▴ 30
3
votes
3
replies
1.8k
views
How to merge several BED files to create a comprehensive overview file
pandas granges python bioconductor
updated 4.5 years ago by 14k • written 4.5 years ago by ▴ 60
0
votes
0
replies
684
views
GEMINI (GEnome MINIng) inheritance pattern command warning no affecteds in family 0
ubuntu GEnomeMINIng gemini
4.5 years ago by taniamahmood38 ▴ 60
0
votes
0
replies
548
views
Tped file locus column to gene
plink
4.5 years ago by storm1907 ▴ 30
19
votes
11
replies
21k
views
6 follow
Get Gene Symbol Synonyms/Aliases With Biomart
biomart gene
updated 4.5 years ago by 89k • written 13.8 years ago by ★ 1.0k
2
votes
4
replies
1.8k
views
Trimmomatic not recognising both adapters
trimmomatic adapters
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
0
votes
1
reply
699
views
How to convert a value of columnA to a value of columnB (in R)?
R
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 70
0
votes
0
replies
695
views
Error in cut edge program in MATLAB
function programming
4.5 years ago by Abhinav • 0
0
votes
1
reply
871
views
what is the difference between cell lines and tissue when doing sequencing analysis
dna mapping sequence
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
0
votes
0
replies
733
views
The number of predicted CDS/ORF does not match with the annotated ones (KEGG-GHOSTKOALA)
gene KEGG alignment rna genomics
4.5 years ago by shail.nair05 ▴ 20
1
vote
1
reply
1.5k
views
Understanding blast2go annotation result
combinedGOgraph annotation blast2go
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 110
4
votes
3
replies
4.3k
views
How to remove multiple adapter sequences by Cutadapt
RNA-seq cutadapt adapter multipleadapters
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 40
0
votes
4
replies
2.1k
views
Computing Hamming similarity (opposite of distance) between string P and each position in string T
alignment scoring programming
4.5 years ago by lehuyduc3 • 0
1
vote
2
replies
1.3k
views
How can I get GTF file for TE annotations from Helicoverpa armigera?
genome workflow database pipeline
4.5 years ago by pavelasquezv ▴ 50
1
vote
1
reply
1.0k
views
Interpret Bedtools Overlap?
bed
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 100
2
votes
3
replies
2.7k
views
Is there a way to convert rpkm data to raw counts
rna
4.5 years ago by rishav513 ▴ 30
11
votes
10
replies
22k
views
ENSMUSG number convert to gene name
ensembl gene
updated 2.8 years ago by 89k • written 4.5 years ago by ▴ 250
9
votes
4
replies
16k
views
Interpretation of Principal component analysis
clustering
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 60
8
votes
9
replies
7.9k
views
8 follow
Issue With CRAM -> BAM -> FASTQ Conversion
samtools fastq cram bam view
updated 2.4 years ago by • 0 • written 6.2 years ago by ▴ 20
0
votes
0
replies
1.1k
views
bootstrapping genomes for demographic analysis
bootstrapping genome bootstrap demography
4.5 years ago by truebeliever24 ▴ 50
0
votes
0
replies
797
views
Combine populations.samples.fa alleles using STACKS
rad snp haplotype vcf
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
3
votes
3
replies
1.6k
views
MACS2
mapping
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 10
1
vote
2
replies
1.3k
views
Clustering two different RNA-seq timeseries results to identify shared/opposite gene patterns?
RNA-seq clustering time-series
updated 2.3 years ago by 45k • written 4.5 years ago by ▴ 210
2
votes
6
replies
3.0k
views
Modify chromosome column in bam file using pysam fetch
pysam
updated 4.5 years ago by ▴ 170 • written 4.5 years ago by ▴ 80
121,907 results • Page 685 of 2439
Recent Votes
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
Comment: Automatically annotating a feature using a genbank file
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Popular Question to alison.ludzki • 0
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Recent Replies
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.
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…
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