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121,907 results • Page 38 of 2439
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0
votes
4
replies
1.0k
views
bcftools not calling variants that appear high quality
bcftools DNAseq snps
updated 7 months ago by 166k • written 7 months ago by ▴ 20
0
votes
1
reply
650
views
Gene ontology and NCBI blast analysis
gene-ontology protein-sequence blast
updated 7 months ago by 103k • written 7 months ago by • 0
0
votes
0
replies
454
views
Exact steps to calculate the SNP index to identify locality of EMS induced mutation
samtools bcftools index SNP
7 months ago by n.anuragsharma ▴ 40
0
votes
3
replies
895
views
How to download metadata from SRA database
metadata Sra download
updated 7 months ago by ★ 2.1k • written 7 months ago by • 0
0
votes
3
replies
846
views
Trouble using sortmerna: How to get nonrRNA output from paired fastq files
rnatranscripts sortmerna fastq
updated 7 months ago by 153k • written 7 months ago by ▴ 10
2
votes
5
replies
1.0k
views
Gene expression of a particular gene
gene-expression DESeq2 RNASeq
updated 7 months ago by 5.8k • written 7 months ago by ▴ 70
1
vote
1
reply
669
views
What are the risque of keeping variants which read have low mapping quality?
gatk mutect2 bwa variant-calling
updated 7 months ago by 45k • written 7 months ago by ▴ 120
0
votes
2
replies
1.5k
views
SQK-LSK112 adapter sequences
Nanopore
updated 7 months ago by • 0 • written 3.0 years ago by ▴ 50
3
votes
3
replies
1.0k
views
Using COUNT with bcftools filter
bcftools vcf filter
7 months ago by mykle hoban ▴ 40
1
vote
1
reply
581
views
mafft --auto alignment
--auto alignment mafft
updated 7 months ago by ▴ 80 • written 7 months ago by • 0
0
votes
0
replies
981
views
Job: Bioinformatician - South Australian Genomics Centre (SAGC) at SAHMRI
Bioinformatician
7 months ago by Careers@SAHMRI ▴ 50
0
votes
4
replies
1.2k
views
Check the normalizations available in a hic file?
juicer-tools hic-pro hic
7 months ago by rls_08 ▴ 40
4
votes
0
replies
459
views
Tool: High Resolution Imaging of Illumina Flowcell Surface Properties
Illumina NovaSeqX bbtools
7 months ago by Brian Bushnell 20k
4
votes
2
replies
747
views
identifying 3'utrs for multiple transcripts of genes from a summarized experiment.
biomart transcriptome utr
7 months ago by RNAseqer ▴ 280
1
vote
1
reply
610
views
ChIPSeeker not annotating with hg38, stuck on hg19
CHiPseeker ATAC-Seq
updated 7 months ago by 153k • written 7 months ago by • 0
0
votes
1
reply
392
views
I cannot obtain my counts in galaxy server
galaxy
updated 7 months ago by 45k • written 7 months ago by • 0
0
votes
6
replies
985
views
Illumina HumanHT-12 V4.0 analysis but I only have the .IDAT files
Illumina Expression-Analysis Microarray
updated 7 months ago by ★ 2.1k • written 7 months ago by • 0
1
vote
0
replies
478
views
edgeR questions for use with cytometry counts
edgeR cytometry diffcyt
7 months ago by SamGG ▴ 150
12
votes
6
replies
1.3k
views
6 follow
Analyze read lengths in Illumina data
human illumina libraries
updated 7 months ago by 166k • written 7 months ago by ▴ 10
6
votes
3
replies
1.0k
views
Convert Long Nanopore reads to Illumina Paired end reads
illumina sequencing reads nanopore
updated 7 months ago by 166k • written 7 months ago by ▴ 60
0
votes
0
replies
297
views
(Too?) Simple Deep Mutational Sequencing pipeline for fastq to enrichment score
deep-mutational-sequencing enrichment-score
7 months ago by Flipstone • 0
2
votes
1
reply
643
views
Seeking Public Nanopore Datasets (FAST5 + FASTA/FASTQ) for DNA Storage Research
Nanopore-Sequencing Machine-Learning FAST5 DNA
updated 7 months ago by 45k • written 7 months ago by • 0
0
votes
3
replies
766
views
Umi_tools regex blank output
regex umi_tools
7 months ago by amyruthvandiver • 0
0
votes
0
replies
341
views
RAxML or BV-BRC tree
RAxML tree Phylogenic BV-BRC
7 months ago by anna • 0
0
votes
0
replies
421
views
Choosing the better input files for COGclassifier tool
classifier COG
7 months ago by anna • 0
0
votes
0
replies
338
views
Anti-ligand , receptor blocking and cell cell interaction analysis
cellchat cell nichenet single
7 months ago by carolofharvest ▴ 50
0
votes
0
replies
1.0k
views
How can I linearize certain segments within an existing protein structure constraining to volumetric grids using PyMOL scripting?
python protein-structure structural-bioinformatics protein
7 months ago by Aman Vishwakarma ▴ 10
5
votes
5
replies
1.1k
views
Overlapping regions in bedGraph
bedGraphToBigWig bedGraph
updated 7 months ago by 45k • written 7 months ago by • 0
4
votes
3
replies
2.2k
views
How to estimate and visualize haplotype blocks on a phased VCF/BCF
haplotype vcf
updated 9 days ago by ★ 4.3k • written 2.9 years ago by ★ 5.4k
1
vote
3
replies
582
views
Low RIN, novel samples
RIN RNA
7 months ago by Emilie ▴ 10
6
votes
7
replies
1.1k
views
Why don't mRNA levels measure protein synthesis rates?
mRNA translation protein-synthesis rnaseq
updated 7 months ago by 45k • written 7 months ago by ▴ 40
5
votes
9
replies
1.4k
views
Drosophila melanogaster dm3 intron percentage too high
drosophila sequence nucleotide intron genomics
updated 7 months ago by 103k • written 7 months ago by ▴ 20
0
votes
3
replies
1.2k
views
Finding high number of significant genes by FindMarkers by Seurat
FindMarkers Single-cell Seurat
updated 7 months ago by ★ 19k • written 7 months ago by • 0
1
vote
3
replies
749
views
What is the next step after getting the raw counts matrix for RNA-seq data?
DESEq2 transriptomics RNA-seq
updated 7 months ago by 103k • written 7 months ago by ▴ 70
3
votes
11
replies
3.3k
views
How can I linearize certain residues within an existing protein structure to create a dumbbell-shaped structure?
pymol python biopython structural-bioinformatics
7 months ago by Aman Vishwakarma ▴ 10
0
votes
1
reply
1.3k
views
codon adaptation index (CAI) estimation
codon-usage
updated 7 months ago by 45k • written 5.9 years ago by ▴ 90
0
votes
3
replies
740
views
High adj. p-value/FDR despite large FC and high expression levels
edgeR DESeq2 RNA-Seq
updated 7 months ago by ▴ 820 • written 7 months ago by ▴ 10
0
votes
1
reply
469
views
Why Is My Uniquely Mapped Read Count Higher in Samtools Compared to Bowtie2?
Bowtie2
updated 7 months ago by 103k • written 7 months ago by ▴ 10
0
votes
0
replies
235
views
XR-seq processing pipeline
XR-seq
7 months ago by sleepystudent • 0
0
votes
0
replies
274
views
Smart-Seq3 intron+exon meaning
exon R smart-seq3 plots intron
7 months ago by Evlampia • 0
0
votes
0
replies
264
views
I'm not sure what is going on with my DEXSeq object
GenomicRanges DEXSeq Help RNA-Seq SummarizedExperiment
7 months ago by cftattersfield • 0
0
votes
1
reply
575
views
ChIP-seq signal across bed regions
normalisation chipseq quantification signal
updated 7 months ago by ★ 2.0k • written 7 months ago by • 0
2
votes
2
replies
666
views
Reading location of a feature of a miRNA entry in miRBase in EMBL format
format miRBase EMBL
7 months ago by Coleman • 0
0
votes
3
replies
964
views
How can you interpret a phased VCF with no "phase set" field (PS)
variants vcf phasing genotyping
7 months ago by cmdcolin ★ 4.3k
2
votes
6
replies
1.2k
views
How to make a .gaf file for GO analysis
NGS GO
7 months ago by noodle ▴ 650
0
votes
5
replies
928
views
bigWig size difference between variableStep and fixedStep wig files
bigWig wig
7 months ago by notthebmovieactor • 0
0
votes
6
replies
932
views
Unannotated reads through STAR
STAR IGV Unannotated-reads
7 months ago by rajdeepboral00 ▴ 70
0
votes
2
replies
477
views
multiple outputfiles after bamtofastq for same library
cellranger 10x bamtofastq
updated 7 months ago by 153k • written 7 months ago by ▴ 30
2
votes
6
replies
925
views
Hisat2 index genome
hisat2
7 months ago by frarodmar17 • 0
28
votes
22
replies
65k
views
22 follow
Public Electronic Health Records Database
database
written 12.4 years ago by ★ 1.6k
121,907 results • Page 38 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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Popular Question to Pranava ▴ 10
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Recent Replies
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…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
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