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121,908 results • Page 689 of 2439
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1
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2
replies
1.6k
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How to get raw read counts of genes/cds/transcripts from SAM/BAM file?
RNA-Seq alignment gene sequencing assembly
4.5 years ago by shail.nair05 ▴ 20
2
votes
4
replies
2.3k
views
How to install Jellyfish in Windows 10?
general
updated 4.5 years ago by ★ 19k • written 4.5 years ago by ▴ 10
0
votes
1
reply
1.0k
views
The effect of metabolomics on other omics
metabolomics multiomics
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 80
0
votes
2
replies
923
views
Figure for relative error with large database
python data
4.5 years ago by Evy_00 • 0
0
votes
0
replies
977
views
LD pruning parameters
linkage pruning plink
4.5 years ago by anithanagaraj93 ▴ 10
0
votes
17
replies
4.1k
views
I am not able to let R read my file
R fasta
updated 4.5 years ago by 3.4k • written 4.5 years ago by • 0
0
votes
1
reply
966
views
Trouble in SNP calling using GATK HaplotypeCaller
gatk genome
updated 4.5 years ago by ▴ 940 • written 4.5 years ago by • 0
4
votes
2
replies
2.2k
views
"heightweight" R-dataset data-structure?
heavyweight R-language
4.5 years ago by natasha.sernova ★ 4.0k
1
vote
2
replies
1.2k
views
How to do clustering of SNPs according to linkage disequilibrium (r2) values?
nex-gen R rna-seq snp genome
3.2 years ago by anikcropscience ▴ 270
0
votes
0
replies
804
views
Getting distance matrix from specific models for AA/Nt MSA
msa distancemodels raxml python biopython
4.5 years ago by Klios3th • 0
0
votes
1
reply
1.3k
views
Altering a python script to calculate GC content
sequence
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 70
0
votes
0
replies
788
views
Job: Two postdocs (one wet, one dry) in 3' UTR biology and RNA threapeutics
rna machine-learning utr
4.5 years ago by i.sudbery 22k
0
votes
3
replies
2.5k
views
What is the error of this Nexus file? I cannot open it in Figtree
figtree ggtree R phylogenetics
4.5 years ago by fhsantanna ▴ 620
0
votes
3
replies
1.0k
views
Risk calculation in pedigrees
genome
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 30
0
votes
0
replies
611
views
Altering a python script to calculate GC content
sequence
4.5 years ago by dk0319 ▴ 70
0
votes
1
reply
824
views
identify most variable bacteria within microbiome longitudinal data
microbiome longitudinal data statistics R
updated 4.5 years ago by 20 • written 4.5 years ago by ▴ 30
0
votes
0
replies
1.1k
views
How to instsall "Structure 2.3" for windows 10, 64bit
software error
4.5 years ago by hosin • 0
0
votes
1
reply
705
views
Nanopore data error
RNA-Seq
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 30
0
votes
1
reply
700
views
Having issues with having extra information on my Fasta file.
sequence
4.5 years ago by trejomarco6 • 0
9
votes
5
replies
3.5k
views
Forum: Should I get my MS in Bioinformatics at UCSC or GA Tech
genome
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 10
0
votes
2
replies
1.5k
views
Lengths of UTR3, UTR5 and ORF from gtf file
UTR ORF
4.5 years ago by bio_elle ▴ 10
0
votes
4
replies
1.5k
views
Plotting PCA and Admixture for CNVs
R
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
2
votes
4
replies
1.8k
views
How to download viral subset of the UniProt Reference Clusters?
swissprot database uniprot
updated 4.4 years ago by ★ 2.4k • written 4.5 years ago by ▴ 60
0
votes
1
reply
2.3k
views
Dispersion and variance in RNA-seq explained.
RNA-Seq
updated 3.6 years ago by 45k • written 4.5 years ago by ▴ 140
0
votes
0
replies
1.1k
views
How do I solve "incompatible numba" while installing Scanpy?
RNA-Seq alignment
4.5 years ago by Olalekan • 0
0
votes
3
replies
2.4k
views
antismash 5.0 (New region concept) - counting BGCs
antismash metagenomics
updated 4.5 years ago by ▴ 140 • written 5.0 years ago by ▴ 110
0
votes
0
replies
1.1k
views
merge DRAGEN vcf
structuralvariants DRAGEN mergevcf
updated 4.5 years ago by 14k • written 4.5 years ago by • 0
0
votes
0
replies
1.0k
views
How to interpret output of SAM/SAMseq in R (samr package)
R
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 110
0
votes
0
replies
994
views
SAM: why NM and MD tag are changed by the picard tool SetNmMdandUqtag ?
alignment gatk sam
4.5 years ago by quentin54520 ▴ 120
0
votes
3
replies
795
views
emboss skipredundant issue
alignment sequence
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
0
votes
0
replies
759
views
ENSEMBL bigwig RNA-seq tracks for single-gene visual inspection
RNA-Seq tracks bigwig ensembl zebrafish
4.5 years ago by bernarda • 0
0
votes
2
replies
1.2k
views
Which Bioinformatic tools are used for NRPS Domain analysis?
NRPS NRPS analysis Domain prediction
updated 4.5 years ago by ▴ 140 • written 6.5 years ago by • 0
9
votes
3
replies
1.6k
views
Should I contact an author if I can (or cannot) find their data ?
reads dataset publication
updated 4.5 years ago by 56k • written 4.5 years ago by ▴ 20
1
vote
2
replies
1.5k
views
Does Jellyfish k-mer counting tool give wrong k-mers?
software error
4.5 years ago by rubyeat88 ▴ 10
1
vote
2
replies
888
views
Want to know whether this p-adj value is acceptable
RNA-Seq next-gen sequencing
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 10
50
votes
20
replies
8.2k
views
18 follow
Forum: Explain bioinformatics to a 10 year old
bioinformatics
updated 2.5 years ago by 45k • written 9.5 years ago by ★ 1.1k
0
votes
0
replies
596
views
Gene Ontology with Locus referring
GO gene
4.5 years ago by rrapopor ▴ 40
0
votes
0
replies
676
views
Plotting PCA and Admixture for CNVs
genome
4.5 years ago by hosin • 0
0
votes
2
replies
1.1k
views
Discrepancy between Genome Browser hg19 phyloP Score and that of wig data
phyloP genome browser
4.5 years ago by progistar ▴ 40
2
votes
2
replies
5.0k
views
Whole Blood Gene Expression Deconvolution
expression
updated 4.5 years ago by 20 • written 11.5 years ago by ▴ 90
1
vote
5
replies
2.1k
views
chi squared assesment of gene expression and batch effect
RNA-Seq r chi squared
4.5 years ago by RNAseqer ▴ 280
0
votes
1
reply
1.4k
views
model matrix error message 'unequal columns/rows' when using a conditional variable
rna-seq categorical variables edger
updated 4.5 years ago by ★ 8.3k • written 4.5 years ago by ▴ 280
0
votes
5
replies
2.0k
views
I am scaffolding using HiC data and found many contigs are out of the chromosome. Please help me.
sequencing assembly
updated 4.5 years ago by 56k • written 4.5 years ago by • 0
4
votes
3
replies
1.4k
views
Vertically merge dataframes in R from a list
R
4.5 years ago by ellieuk ▴ 40
0
votes
2
replies
1.1k
views
How to make paired-end sequencing multi-mapping reads have only the optimal two reads
RNA-Seq alignment sequencing
4.5 years ago by minghuiguo448 • 0
0
votes
1
reply
960
views
Deletions together with SNVs on BAM files
alignment sequencing genome browser
4.5 years ago by baliczap • 0
2
votes
0
replies
846
views
3D distance between two chromosomal coordinates in 3D human genome?
3d hi-C genome chia-pet
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 20
0
votes
0
replies
766
views
copy number of gene in the gap of segmentation file
WES copy number sequenza
4.5 years ago by xiaoqiaoliu • 0
0
votes
1
reply
863
views
Nesting a covariate for differential expression design
RNA-Seq nested covariates
updated 4.5 years ago by 20 • written 4.6 years ago by ▴ 280
2
votes
2
replies
1.9k
views
Why PLINK is producing different LD result with the same dataset?
SNP sequence genome R software error
updated 4.5 years ago by ★ 4.8k • written 4.5 years ago by ▴ 270
121,908 results • Page 689 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
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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