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121,907 results • Page 684 of 2439
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3
votes
5
replies
3.1k
views
Hi-C: getting intervals from "A Compendium of Chromatin Contact Maps Reveal Spatially Active Regions in the Human Genome"
Hi-C intervals chromosome interaction tad
updated 6.7 years ago by 105k • written 6.7 years ago by 166k
0
votes
4
replies
4.3k
views
SRA tool kit 2.9.4
software error
updated 4.5 years ago by 153k • written 6.6 years ago by • 0
0
votes
0
replies
868
views
Job: Single cell genomic approaches to study mitochondrial genetics and disorders
immunology cellmulti-omics mitochondrialgenetics
4.5 years ago by info ▴ 30
0
votes
1
reply
1.4k
views
Job: Carry out your own PhD project! - In Single Cell Genomics and Mitochondrial Genetics
PhD
updated 2.3 years ago by 45k • written 4.6 years ago by ▴ 30
0
votes
8
replies
2.1k
views
Upload data in tripal
database tripal
4.3 years ago by felipead66 ▴ 120
0
votes
0
replies
1.1k
views
error when using ViSEAGO package
geneontology ViSEAGO
4.5 years ago by peter.berry5 ▴ 60
0
votes
1
reply
884
views
Curate a specific Reference Database only containing species/strains belonging to one bacterial family
RStudio microbiome NGS referencedatabase
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 10
0
votes
2
replies
1.5k
views
I use Mutects of Variant Call for paired Tumor/Normal WES, do I get a credibility (p value) for each call?
Mutect2 GATK WES Funcotator
4.5 years ago by field654 ▴ 30
0
votes
1
reply
1.5k
views
bcftools csq creates no output
genotyping sequencing dna format
4.5 years ago by ommegang ▴ 10
0
votes
0
replies
875
views
News: 3-day ONLINE TRAINING - NEXTFLOW
pipeline programming workflow cloud clustering
updated 4.5 years ago by 153k • written 4.5 years ago by ★ 2.6k
0
votes
0
replies
708
views
What is the best practice for gene tree - species tree reconcilation?
gene-tree phylogenetics species-tree NOTUNG
4.5 years ago by 1099 • 0
1
vote
1
reply
1.2k
views
Calculate allele frequencies per population with SNPRelate
SNPRelate allelefrequencies plink SNP R
updated 4.5 years ago by ▴ 330 • written 4.5 years ago by ▴ 40
0
votes
0
replies
891
views
Job: 2 Postdoctoral fellows in Metabolic Engineering at DTU Biosustain
FACS GC-MS HPLC LC-MS
4.5 years ago by info ▴ 80
1
vote
1
reply
1.0k
views
Use of megSAP
general
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by • 0
0
votes
9
replies
3.1k
views
How to do the gene ontology analysis for the list of genes
R RNAseq geneontology rna goseq
updated 4.5 years ago by 9.0k • written 4.5 years ago by ▴ 20
1
vote
7
replies
3.5k
views
Cutadapt or Trim Galore for SMART-seq?
TrimGalore galaxy SmartSeq rna Cutadapt
4.5 years ago by Youyy • 0
6
votes
6
replies
2.3k
views
plain list of human cell lines
human cell lines
4.5 years ago by bstrs • 0
1
vote
1
reply
893
views
Reasons for drops in alignment
alignment quality
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 760
2
votes
3
replies
2.2k
views
Only a small portion of my reads have Smart-seq adapters, why?
Smartseq RNAseq rna galaxy illumina
4.5 years ago by Youyy • 0
0
votes
0
replies
768
views
Difference between Whole Exome Sequencing Pipeline for IonTorrent and Illumina?
pipeline ngs whole-exome-sequencing
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 20
7
votes
2
replies
25k
views
GRCm39 (mm39) vs GRCm38(mm10)
genome reference mouse DNA dna
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 20
0
votes
5
replies
2.3k
views
mapping unavailable in Blast2GO
mapping blast
updated 4.5 years ago by 15k • written 4.5 years ago by • 0
0
votes
1
reply
1.3k
views
Distance Matrix Calculation
genome biopython
updated 4.5 years ago by ★ 2.2k • written 4.5 years ago by ▴ 140
0
votes
0
replies
734
views
Identification of paralogs having parental/daughter relationship
paralogs
4.5 years ago by arsala521 ▴ 60
2
votes
1
reply
1.7k
views
BWA-MEM or BWA-ALN + BWA-SAMSE for MGI sequencing
bwa ali sequencing
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
3
votes
4
replies
1.5k
views
Alignment Viewer
sequencing alignment
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 40
3
votes
17
replies
3.9k
views
FAIRE for non-standard cultivar, mapping to reference, MAPQ
sequencing faire mapping
4.5 years ago by boczniak767 ▴ 880
0
votes
1
reply
3.3k
views
Regarding valid transcript and Transdecoder output
sequencing Transdecoder transcript assembly
updated 4.5 years ago by ▴ 590 • written 9.4 years ago by ★ 1.9k
0
votes
2
replies
2.8k
views
GAPIT error : invalid '(to - from)/by'
GWAS R programming
4.5 years ago by Inquisitive8995 ▴ 280
3
votes
2
replies
7.3k
views
Pheatmap/Complexheatmap: making a continuous color scale with NAs
clustering pathways complexheatmap pheatmap
4.5 years ago by Ridha ▴ 130
1
vote
2
replies
1.6k
views
Recommended pipeline for Cut&Run
pipeline
updated 3.9 years ago by • 0 • written 4.5 years ago by ▴ 30
2
votes
3
replies
2.0k
views
BAM file download for just a few genes
RefSeq BAM position RNA-Seq UCSC
updated 4.5 years ago by 14k • written 4.5 years ago by ▴ 110
22
votes
19
replies
7.8k
views
7 follow
FastQTL - GNU Scientific Library (GSL) Domain Error
eQTL GSL RNA-Seq SNP FastQTL
updated 4.5 years ago by • 0 • written 8.6 years ago by ▴ 170
5
votes
4
replies
15k
views
samtools multithreads
samtools
4.5 years ago by Palgrave ▴ 140
2
votes
4
replies
1.7k
views
How to extract the mean quality score of RNAseq for a sample?
FastQC RNAseq Cutadapt illumina galaxy
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
0
votes
7
replies
3.3k
views
Cannot resize rowlabels in aheatmap
clustering aheatmap R
updated 4.5 years ago by 5.8k • written 4.5 years ago by ▴ 20
2
votes
2
replies
2.1k
views
Survival analysis
Cutoff TCGA
updated 4.5 years ago by 5.8k • written 4.5 years ago by ▴ 40
0
votes
4
replies
2.5k
views
Gene ID conversion for pathway enrichment analysis of differentially expressed genes
Pathwayenrichment GeneIdconversion
updated 3.8 years ago by 4.8k • written 4.5 years ago by ▴ 20
0
votes
0
replies
811
views
News: BioSoftics- An Innovative way to explore Science and Technology
genome Biotechnology
updated 4.2 years ago by 45k • written 4.5 years ago by ▴ 10
1
vote
4
replies
2.7k
views
vcftools --TajimaD does not start at 0 and misses variants
vcftools tajimaD
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 40
0
votes
1
reply
913
views
Missing K-mer in Text
genome alignment
updated 4.5 years ago by 56k • written 4.5 years ago by ▴ 30
2
votes
13
replies
5.2k
views
Get unmapped reads from cram/bam file
alignment
updated 4.5 years ago by 89k • written 4.5 years ago by ▴ 140
4
votes
6
replies
2.1k
views
How can I solve the following error? No module named commons.core.LoggerFactory
python
4.5 years ago by pavelasquezv ▴ 50
2
votes
1
reply
1.6k
views
bedtools getfasta command
fasta
updated 4.5 years ago by ★ 3.9k • written 4.5 years ago by ▴ 40
0
votes
1
reply
891
views
Mendelian vs Inherited variants
inherited mendelian
updated 4.5 years ago by ★ 3.0k • written 4.5 years ago by ▴ 30
2
votes
3
replies
5.5k
views
Converting merged Seurat object back to dgCMatrix
Seurat
4.5 years ago by LacquerHed ▴ 30
5
votes
5
replies
11k
views
Using Seurat to take in a Normalised TPM Gene to Cell matrix as a Seurat Object
format sequencing rna
updated 4.3 years ago by ★ 19k • written 4.5 years ago by • 0
1
vote
2
replies
4.4k
views
Interpreting trim_galore report
RNA-Seq
updated 4.5 years ago by 153k • written 8.1 years ago by ▴ 20
0
votes
1
reply
1.2k
views
2 transcript_id values for the same tRNA in GTF file
GTF arabidopsisthaliana annotation
updated 4.5 years ago by 5.8k • written 4.5 years ago by • 0
2
votes
2
replies
1.1k
views
reformat eland_result.txt to MACS input file
format
updated 4.5 years ago by 103k • written 4.5 years ago by • 0
121,907 results • Page 684 of 2439
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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
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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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…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
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