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121,908 results • Page 687 of 2439
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3
votes
6
replies
2.6k
views
DEG but counts in only one sample!
deseq2 rnaseq degs yeast
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 40
5
votes
9
replies
4.7k
views
Unable to install DiffBind and DESeq2 4.0.3 and 4.0.4 (Package not available on these version of R error)
ChIP-Seq
updated 4.5 years ago by ▴ 40 • written 4.5 years ago by • 0
2
votes
4
replies
4.0k
views
How to sort vcf file
vcf
4.5 years ago by shubhamkumbhar420 ▴ 40
3
votes
3
replies
5.6k
views
Installing SRAToolKit
programming general
updated 4.5 years ago by ▴ 370 • written 4.5 years ago by ▴ 10
1
vote
1
reply
1.4k
views
RSEM to CPM?
rna RNA
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 10
8
votes
19
replies
6.3k
views
How to design a Volcano plot
EnhancedVolcano
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
1
vote
0
replies
872
views
Forum: Sharing frequently asked questions about microbial genome sequencing I
sequencing microbial faq genome BI
4.4 years ago by Novogene ▴ 510
0
votes
0
replies
675
views
Identify cell type from bulk RNA sequencing data
sequencing type clustering r
4.5 years ago by minoo ▴ 10
1
vote
6
replies
2.1k
views
how to extract content from dbSNP database using set of "rsid's".
dbSNP rsid dataretrieval database snp
4.5 years ago by deepak.deucy ▴ 10
0
votes
0
replies
1.0k
views
KING relationship inference, problem with sheep population
king kinship snp sheep genome
4.5 years ago by maxysha95 • 0
0
votes
2
replies
1.3k
views
TE identification & classification via signal processing techniques?
discovery transposon transform classification
4.5 years ago by gnmcsbnfrmtcsclb ▴ 70
0
votes
0
replies
865
views
Using SAIGE for GWAS without including covariates
SNP GWAS vcf plink SAIGE
4.5 years ago by mfshiller ▴ 20
2
votes
4
replies
1.9k
views
Blast command use
blast
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 40
0
votes
20
replies
3.6k
views
Mixed Linear Model and GWAS study
GWAS SNPs Mixed Liner Model TASSEL
4.5 years ago by Kumar ▴ 170
0
votes
0
replies
950
views
How to add legend in Adegenet at R
GWAS SNPs R
4.5 years ago by Kumar ▴ 170
5
votes
2
replies
1.4k
views
hmmer identical target and query proteins
hmmer hmm hmmsearch
4.5 years ago by mnsp088 ▴ 100
2
votes
3
replies
1.3k
views
search of genomic annotation databases
genomics annotation
4.5 years ago by Rima ▴ 20
1
vote
3
replies
1.3k
views
Is there any way to get the mismatch positions in the reads mapped by the Bowtie2 ?
sequence mapping alignment genomics
updated 4.5 years ago by 103k • written 4.5 years ago by • 0
1
vote
1
reply
1.1k
views
How to perform custom annotation using garfield_annotate_uk10k.sh script in GARFIELD tool?
R bash awk GWAS
updated 15 months ago by 45k • written 4.5 years ago by ★ 3.1k
3
votes
1
reply
1.5k
views
Get all unmapped read and mate in bam
aligner genomics dna
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Altering bioawk script to take list.txt file as a command line parameter
bash shell-script
updated 2.8 years ago by 45k • written 4.5 years ago by ▴ 70
2
votes
1
reply
1.1k
views
Orthology and sequence identity/similarity
identity similarity orthology homology
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ★ 2.9k
6
votes
0
replies
3.4k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
4.5 years ago by rpolicastro 13k
2
votes
3
replies
1.5k
views
DNA sequence simulator with different mutations rate per region
dna simulation mutation
updated 4.5 years ago by 103k • written 4.5 years ago by ★ 2.9k
1
vote
4
replies
11k
views
understanding the output files of fasterq-dump --split-files
fasterq-dump
updated 4.5 years ago by 45k • written 7.1 years ago by • 0
3
votes
4
replies
2.1k
views
How do we handle TPM values after converting from Ensembl to HUGO genes?
ensembl hugo tpm-calculator tpm rna-seq
updated 4.5 years ago by 103k • written 4.5 years ago by ★ 1.3k
4
votes
7
replies
4.2k
views
How to use Bowtie to align a list of fasta sequence to a reference genome?
mapping genome alignment fasta genomics
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 270
5
votes
3
replies
1.9k
views
What Machine Learning, AI, Deep Learning, & Neural Network Python packages do you use in Bioinformatics and/or whole genome sequencing annotation?
data python sequencing
updated 4.5 years ago by ★ 19k • written 4.5 years ago by ▴ 20
1
vote
0
replies
840
views
Empty result obtained when using SAMTOOLS and MPILEUP to generate consensus sequences FASTQ file
sequencing fasta fast dna
4.5 years ago by roelofco ▴ 10
1
vote
3
replies
9.3k
views
Update FAM file Plink for fid and pheno
FID fam plink phenotype
updated 4.5 years ago by 11k • written 4.5 years ago by • 0
0
votes
3
replies
1.3k
views
Could direction of reads affect the mapping of medium-size insertions
tmap INDELS
updated 4.5 years ago by 103k • written 4.5 years ago by • 0
1
vote
3
replies
3.2k
views
RSEM error: The adjacent two lines do not represent the two mates of a paired-end read!
rna alignment aligner
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 30
1
vote
0
replies
1.8k
views
Job: Computational Research Scientist: JG-Joint Genome Institute
general
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 70
0
votes
0
replies
1.6k
views
Job: Data Scientist: JG-Joint Genome Institute
genomics
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 70
0
votes
5
replies
2.1k
views
Issues with Centrifuge indexing
Centrifuge data
4.5 years ago by mcclurejenniferc • 0
2
votes
3
replies
2.6k
views
Explanation of Venn diagram output
general education
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 30
0
votes
0
replies
1.7k
views
Job: Computational Biology Program Developer
programming
4.5 years ago by BerkeleyLab ▴ 70
2
votes
3
replies
3.0k
views
Michigan imputation server quality control failed
imputation genotype
updated 4.5 years ago by 2.9k • written 6.5 years ago by ▴ 100
0
votes
0
replies
627
views
TWAS-hub interpretation: positive and negative values
hub twas
4.5 years ago by Friyunnwoo ▴ 20
6
votes
2
replies
2.6k
views
bcftools vcf2sex
genomics genome alignment genotyping
updated 4.5 years ago by ★ 1.5k • written 4.5 years ago by ▴ 540
2
votes
3
replies
2.6k
views
Alternatives to cytoscape for integrative analysis of Rna-seq data
rna-seq enrichment
updated 4.5 years ago by ▴ 130 • written 4.5 years ago by ▴ 10
4
votes
8
replies
9.0k
views
8 follow
Can not pass QC when doing imputation with Michigan Imputation Serve and Haplotype Reference Consortium panels
HRC 23andme imputation genotype
updated 3.2 years ago by 45k • written 9.6 years ago by ▴ 60
0
votes
0
replies
476
views
Database and webtools to analyze Barrett's esophagus
database genomics gene
4.5 years ago by Eko • 0
17
votes
14
replies
12k
views
11 follow
how to split multi-fasta file into single fasta file named by header
genome perl python3 bash python
updated 15 months ago by 8.7k • written 4.5 years ago by ▴ 120
0
votes
0
replies
802
views
Visualisation of BGCs cluster on Antismash
antismash
4.5 years ago by Rima ▴ 20
0
votes
2
replies
1.8k
views
What is the best tools for circRNA analysis (extraction and quantification) ?
programming rna workflow
4.5 years ago by chloelaloe • 0
0
votes
0
replies
672
views
Taxonomic Bar Plots for too many values
taxonomy
updated 2.7 years ago by 45k • written 4.5 years ago by • 0
1
vote
2
replies
1.5k
views
Can I control the exposure time as a batch effect?
batch-effect RNA-seq time-series deseq2
updated 2.3 years ago by 45k • written 4.5 years ago by ▴ 190
2
votes
4
replies
1.8k
views
GTF format feature definitions
annotation
updated 4.5 years ago by 22k • written 4.5 years ago by ▴ 110
0
votes
4
replies
2.2k
views
Error in apply(counts, 2, function(x) rpkm(x, lengths)) : dim(X) must have a positive length
Rscript R
4.5 years ago by shail.nair05 ▴ 20
121,908 results • Page 687 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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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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