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0
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1.1k
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adjust size of png images in a rasterGrob object
rasterGrob PNG Rmarkdown layout
4.5 years ago by Assa Yeroslaviz ★ 1.9k
2
votes
2
replies
1.2k
views
Mapping after WGS show a parabel form
WGS mapping SNP CNV
updated 4 months ago by ▴ 20 • written 4.5 years ago by ★ 1.9k
3
votes
1
reply
966
views
Can someone recommend a bioinformatics book that is programming oriented?
python
updated 4.5 years ago by ▴ 270 • written 4.5 years ago by • 0
8
votes
5
replies
5.3k
views
Can someone explain in detail the meaning of a gseaplot in GSEA
gseaplot
updated 4.5 years ago by ▴ 270 • written 5.4 years ago by ▴ 400
0
votes
1
reply
2.5k
views
Na (No Value) In Chromosome In Output Snp Test
chromosome
updated 4.5 years ago by • 0 • written 11.8 years ago by • 0
3
votes
2
replies
1.5k
views
qualimap2 mean mapping quality
alignment
updated 4.1 years ago by ▴ 10 • written 4.5 years ago by ▴ 30
11
votes
4
replies
1.6k
views
How to determine % similarity between genomes?
mauve mugsy genome-alignment
updated 2.0 years ago by 45k • written 4.5 years ago by ▴ 170
0
votes
0
replies
749
views
Augustus training with partial transcriptome?
augustus maker maker2 annotation
4.5 years ago by DNAlias ▴ 40
3
votes
3
replies
1.4k
views
Help regarding RNAseq data analysis.
RNA-Seq alignment next-gen
updated 4.5 years ago by 20 • written 6.2 years ago by ▴ 20
2
votes
3
replies
1.4k
views
How to export STAR alignment output files
RNA-Seq
updated 4.5 years ago by ★ 1.5k • written 4.5 years ago by ▴ 10
0
votes
0
replies
733
views
What do the + and - mean in KEGG Ortholog combinations under a particular Module?
kegg database module ortholog identifiers
4.5 years ago by O.rka ▴ 750
4
votes
3
replies
3.8k
views
How to get a mapping between KEGG module and KEGG orthologs?
KEGG Annotation Ortholog Module
updated 4.5 years ago by ▴ 270 • written 4.5 years ago by ▴ 750
0
votes
0
replies
886
views
RNA-Seq Deconvolution algorithm for FACS pre-sorted cells
RNA-Seq deconvolution TIMER
4.5 years ago by Stefan • 0
0
votes
2
replies
710
views
How to identify the reads from diffient seq-data is from the same gene?
rna-seq
updated 4.5 years ago by 13k • written 4.5 years ago by • 0
2
votes
2
replies
2.9k
views
Confused about TSS coordinates
ChIP-Seq
updated 4.5 years ago by ▴ 20 • written 6.2 years ago by ▴ 70
0
votes
0
replies
905
views
Covariates on non-phenotype fam file?
plink genotyping covariates
4.5 years ago by kstafford32 • 0
0
votes
2
replies
1.2k
views
I need to visualize the correlation in better way
multi-omics
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 80
0
votes
1
reply
645
views
RNA Seq Classification
RNA-Seq
4.5 years ago by mosquitoking • 0
0
votes
0
replies
529
views
deduce haplotypes from genotypes
clarks algorithm
updated 4.5 years ago by 20 • written 4.6 years ago by • 0
1
vote
2
replies
1.1k
views
How to make co expression analysis with normalised count rna seq data
R rna-seq
updated 4.5 years ago by ▴ 940 • written 4.5 years ago by ▴ 30
12
votes
8
replies
7.1k
views
Is there a way to visualize log fold changes for Reactome pathways in R?
pathview RNA-Seq reactome bioconductor
updated 4.5 years ago by ▴ 440 • written 6.4 years ago by ▴ 180
0
votes
1
reply
1.1k
views
Is there any way to access the --cores argument in a snakemake workflow?
snakemake
updated 3.7 years ago by ▴ 190 • written 4.5 years ago by ▴ 890
2
votes
2
replies
945
views
Sequencing Information from BAM file
RNA-Seq BAM alignment Library
4.5 years ago by MarVi ▴ 30
8
votes
10
replies
2.2k
views
Performing Differential expression analysis using DESeq with 3 conditions
RNA-Seq Deseq2 R next-gen bioconductor
4.5 years ago by bionewbie • 0
0
votes
2
replies
914
views
Identifiying SNP frequencies for very specific subpopulations on dbSNP
SNP
4.5 years ago by Michael ▴ 290
3
votes
3
replies
2.4k
views
Counts alongside Fold changes - FindMarkers Seurat
RNA-Seq seurat
4.5 years ago by ishwariyavenkatesh • 0
0
votes
0
replies
592
views
Statistical correlation for in-group vs outgroup trait frequencies
statistics p-value spearman correlation
4.5 years ago by leonid.rusin • 0
0
votes
0
replies
615
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
updated 4.5 years ago by 20 • written 4.6 years ago by • 0
2
votes
1
reply
1.4k
views
plink --indep LD calculation and filtering to VCF file in one command
plink
4.5 years ago by rjzotti • 0
1
vote
6
replies
3.3k
views
Setting genotypes to missing for certain positions in vcf file
vcf vcftools
updated 4.5 years ago by 166k • written 4.5 years ago by • 0
6
votes
3
replies
11k
views
The fastest way to download a list of SRR accessions from Sequence Read Archive with sratoolkit
sequence genome
updated 4.5 years ago by ▴ 20 • written 5.7 years ago by ▴ 320
3
votes
2
replies
4.3k
views
Can't create tabix index of the bed file
samtools tabix bed ATAC-seq
updated 4.5 years ago by ▴ 290 • written 4.5 years ago by ▴ 10
0
votes
5
replies
1.3k
views
Shrunk data from Novogene
RNA-Seq
4.5 years ago by Futuremaking • 0
1
vote
2
replies
1.6k
views
scRNA cross-species integration using Seurat v3
integration scRNA-Seq FindIntegrationAnchors
4.5 years ago by maddhesiya13 • 0
5
votes
8
replies
2.3k
views
A layman trying to understand what a FASTA file is
RNA-Seq gene next-gen-sequencing
updated 2.5 years ago by 45k • written 4.5 years ago by ▴ 40
0
votes
3
replies
1.8k
views
change missing genotype in bcf file from 0/0 to ./. to run plink
bcftools plink SNP genotype bcf
4.5 years ago by rah ▴ 30
0
votes
1
reply
2.8k
views
BLAST error: Input db vol size does not match lmdb vol size
BLAST Database Error Protein NR
4.5 years ago by Hansen_869 ▴ 80
3
votes
3
replies
1.4k
views
installation of shovill on windows
software error assembly
updated 4.5 years ago by ▴ 90 • written 4.5 years ago by ▴ 20
0
votes
22
replies
4.2k
views
Specifying database path in BLAST standalone
blast path standalone
4.5 years ago by Hansen_869 ▴ 80
0
votes
0
replies
902
views
Plasmids in the Resfinder tool?
resfinder sequencing antibiotic resistance
4.5 years ago by Researcher ▴ 20
1
vote
1
reply
1.1k
views
CWL workflow - nested_crossproduct output
CWL scatter workflow nested_crossproduct
updated 4.2 years ago by ★ 1.9k • written 4.5 years ago by ▴ 290
2
votes
4
replies
1.2k
views
featurecounts -p Paried ends which count total to use as read1 &read 2 give different totals.
RNA-Seq alignment R gene sequencing
4.5 years ago by ray.liv.wong • 0
3
votes
3
replies
1.2k
views
How can the assumption of a broad/narrow peak be checked?
macs2 ChIP-Seq
4.5 years ago by Aspire ▴ 390
1
vote
1
reply
1.0k
views
variant calling using masked reference genome
Bowtie2 Reference Genome Variant Calling
4.5 years ago by reza ▴ 300
7
votes
11
replies
4.4k
views
What is the appropriate approach for ChIPseq protein genome occupancy % calculation?
ChIP-Seq
updated 2.8 years ago by 45k • written 10.3 years ago by ▴ 120
4
votes
18
replies
4.8k
views
Want to reverse the fasta sequence
fasta
4.5 years ago by harry ▴ 40
2
votes
4
replies
3.2k
views
Read VEP output from command line in R
vep ensembl R Bash
updated 14 months ago by • 0 • written 4.5 years ago by ▴ 100
1
vote
2
replies
863
views
In-silico downsizing to estimate the DNA input
sequencing snp next-gen
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 40
0
votes
6
replies
944
views
How to get related proteins and gene data of an organism (for eg. Lactobacillus )
gene genome
updated 4.5 years ago by 22k • written 4.5 years ago by • 0
3
votes
6
replies
5.3k
views
Is the ENSEMBL FTP down?
ensembl ftp
updated 4.0 years ago by ▴ 940 • written 4.5 years ago by ★ 1.5k
121,908 results • Page 692 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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