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How to compute the "completeness" of a KEGG module using a set of KEGG orthologs? (Module Completion Ratio)
kegg database metagenomics module
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 750
1
vote
5
replies
3.2k
views
Soft-clipping of a BAM file based on regions from the BED file
rna-seq
updated 4.5 years ago by 166k • written 4.5 years ago by ▴ 20
3
votes
2
replies
1.9k
views
Forum: If I want to learn bioinformatics as a computer scientist, would it help to learn Data science and Machine Learning first?
computer-scientist machine-learning
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
2
replies
1.4k
views
Lmfit function, to analyse differential expressions, not coming from arrays
gene
updated 4.5 years ago by 105k • written 4.5 years ago by • 0
0
votes
6
replies
3.0k
views
IDT xGen Exome Research Panel v2 vs Twist Human exome core
next-gen genome sequence
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 20
2
votes
1
reply
911
views
How do I make my code go through all through my list in my file.
sequence
updated 4.5 years ago by 11k • written 4.5 years ago by • 0
1
vote
1
reply
2.3k
views
Download pfam sequence
sequence
updated 4.5 years ago by 20 • written 5.4 years ago by ▴ 140
0
votes
1
reply
1.2k
views
Cheat Sheet for NGS data analysis
next-gen cheat-sheet guidebook pdf NGS
4.5 years ago by angsudas62 • 0
3
votes
5
replies
1.8k
views
Forum: Hide Emails from Guests
meta biostars
updated 2.5 years ago by 45k • written 4.8 years ago by ▴ 840
7
votes
9
replies
1.4k
views
6 follow
Bioinformatics research work
genome snp assembly
updated 4.5 years ago by 56k • written 4.5 years ago by • 0
0
votes
1
reply
1.7k
views
Is there any software/tool that can be used to identify/count the number of feed forward loops and feedback loops in the gene regulatory networks?
Biological Networks Systems Biology
updated 4.5 years ago by 20 • written 8.1 years ago by • 0
0
votes
0
replies
533
views
STRING databases in exome sequencing
genome
4.5 years ago by storm1907 ▴ 30
0
votes
3
replies
924
views
Problem installing bioconductor package 'sesameData' (R 4.0, Bioc 3.12)
R bioconductor sesameData sesame TCGAbiolinks
4.5 years ago by mario.red8976 ▴ 140
5
votes
2
replies
1.8k
views
Question about the sped of the global pairwise alignment of Bio.pairwise.align.globalms and Align.PairwiseAligner()
Python pairwise global aignment
4.5 years ago by master_zhen ▴ 10
0
votes
1
reply
781
views
How to normalise read depth in scRNA-seq data, with usegalaxy
scRNA-seq read-depth
4.5 years ago by ikokkinopoulos • 0
1
vote
3
replies
25k
views
Converting .txt into .fasta
sequence
updated 4.5 years ago by ▴ 20 • written 4.5 years ago by • 0
4
votes
4
replies
2.0k
views
Gene ID problems when mapping and counting
RNA-Seq
4.5 years ago by hellocita ▴ 40
0
votes
0
replies
810
views
Looking to annotate concatenated VCF files on Galaxy for Hg19 reference genome. Need setup guidance.
genome next-gen sequencing sequence gene
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 20
0
votes
1
reply
1.0k
views
Post Alignment basic QC of RNA-Seq data
alignment RNA-Seq
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 80
0
votes
0
replies
1.3k
views
mummerplot - providing ranges for x and y axes
mummer nucmer mummerplot
updated 4.5 years ago by 45k • written 4.6 years ago by ▴ 70
0
votes
0
replies
1.3k
views
Homer annotatePeaks.pl motif density histogram output only showing 0s for motif occurrences
ATAC-seq Homer next-gen ChIP-Seq motif
4.5 years ago by rintsen.sherpa • 0
0
votes
6
replies
8.7k
views
How to keep only Biallelic SNP in vcf
snp
updated 4.5 years ago by 166k • written 4.5 years ago by ▴ 10
0
votes
0
replies
916
views
Color nexus tree automatically using associated data
nexus ape ggtree R python
4.5 years ago by fhsantanna ▴ 620
1
vote
2
replies
1.5k
views
Handling single-cell RNA-seq data with very few cells and possible conversion to bulk-like RNA-seq
RNA-Seq
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
0
votes
0
replies
1.1k
views
Job: Bioinformatics Curator Positions with Computercraft @ NCBI
sequencing
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 90
6
votes
5
replies
4.4k
views
How Do You Align Or Compare Two Networks Content-Wise?
network graphs comparison
updated 4.5 years ago by 20 • written 14.8 years ago by ▴ 990
0
votes
0
replies
1.1k
views
Job: Bioinformatics Data Wrangler with Computercraft @ NCBI
data-wrangler sequencing genome
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 90
0
votes
1
reply
587
views
Checking sequence similarity between 2 RNAseq samples
RNA-Seq genome alignment sequencing
4.5 years ago by Triple Nipple ▴ 10
3
votes
1
reply
3.2k
views
How to speed up computeMatrix of deeptools?
software error
updated 4.5 years ago by ▴ 300 • written 5.2 years ago by ▴ 30
0
votes
2
replies
757
views
Deseq2 with opposite (dominant negative) design
RNA-Seq deseq2 R
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 50
5
votes
5
replies
2.0k
views
NetNGlyc: input sequence names are not unique: What means?
gene sequence glycosilation site-predictor
updated 4.5 years ago by ★ 30k • written 4.5 years ago by • 0
1
vote
4
replies
4.9k
views
Interpration of ridgeplot in transcriptomic analysis
RNA-Seq
updated 20 months ago by 45k • written 4.5 years ago by ▴ 60
4
votes
3
replies
1.6k
views
bowtie2 --passthrough, what does it do???
bowtie2 bowtie
4.5 years ago by mcrepeau ▴ 20
4
votes
6
replies
4.2k
views
Tools for straightforward visualization of alternative splicing events?
RNA-Seq Splicing
written 4.5 years ago by ▴ 40
2
votes
5
replies
3.7k
views
download all metadata from SRA
SRA
4.1 years ago by grant.hovhannisyan ★ 2.6k
0
votes
2
replies
1.9k
views
differential binding analysis of cut-tag peak data
ChIP-Seq
updated 4.5 years ago by 13k • written 4.5 years ago by ▴ 30
1
vote
3
replies
1.1k
views
How to identify 2 genes that have highly identical sequence
gene genome blastn gene identification
4.5 years ago by Ak ▴ 60
2
votes
5
replies
1.4k
views
Gene name put in volcano plot with already have file.
EdgeR volcano
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 40
0
votes
2
replies
1.4k
views
refGene Python Api
python api
4.5 years ago by Bala Hatun • 0
0
votes
0
replies
826
views
How to create marker file for Gistic?
gene gistic
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
2
votes
0
replies
2.3k
views
Confusion over SNP strand importance re genotyping (G>C)
taqman genotyping strand dna SNP
updated 4.5 years ago by 20 • written 9.0 years ago by ▴ 20
1
vote
5
replies
2.3k
views
Replicates do not cluster together
r proteomics
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 40
0
votes
0
replies
935
views
Job: PhD scholarship in bioinformatics in Rostock (Baltic Coast), Germany
aging nutrition
updated 2.5 years ago by 45k • written 4.5 years ago by • 0
0
votes
0
replies
544
views
Should one keep softmasking when combining gff+fasta to gbk format?
annotation
4.5 years ago by robert.murphy ▴ 110
0
votes
0
replies
480
views
Gwas on Window
alignment
updated 4.5 years ago by 166k • written 4.5 years ago by • 0
0
votes
0
replies
772
views
help regarding loading text files in affy package for background correction
R affy textfiles
4.5 years ago by raavi21198 ▴ 20
0
votes
1
reply
603
views
why i don not have peak when use DiffBind
ChIP-Seq
4.5 years ago by 17318598206 ▴ 30
1
vote
1
reply
874
views
how to get the best alignment from the sam file
RNA-Seq alignment
4.5 years ago by minghuiguo448 • 0
4
votes
2
replies
1.9k
views
R with HPC
R
updated 4.5 years ago by 9.0k • written 4.5 years ago by ▴ 30
5
votes
3
replies
1.6k
views
How to download RNA files in the easiest way? (from NCBI's SRA)
RNA-Seq rna-seq next-gen sequencing genome
4.5 years ago by GoldenRetriever ▴ 40
121,908 results • Page 690 of 2439
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Live Online course: Bioinformatic tools for transcriptomic data, Oct 2025
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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