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121,908 results • Page 686 of 2439
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2
votes
6
replies
3.0k
views
Modify chromosome column in bam file using pysam fetch
pysam
updated 4.5 years ago by ▴ 170 • written 4.5 years ago by ▴ 80
0
votes
0
replies
787
views
Quality checking phasing
vcf shapeit phasing
4.5 years ago by truebeliever24 ▴ 50
242
votes
176
replies
114k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 2.3 years ago by 45k • written 10.1 years ago by ★ 4.8k
0
votes
0
replies
1.9k
views
Job: Postdoctoral Fellowship – Machine Learning for Drug Discovery at University of Connecticut
drugdiscovery machinelearning systembiology
4.5 years ago by Minghu • 0
0
votes
1
reply
833
views
How to establish cellular localisation of a protein using STRING?
visualization ppi stringdb cytoscape
updated 4.5 years ago by ▴ 310 • written 4.5 years ago by • 0
1
vote
4
replies
3.9k
views
Annotate Ref/Alt for a list of rsIDs?
dbSNP snp
updated 4.5 years ago by 153k • written 8.0 years ago by ▴ 20
1
vote
4
replies
1.3k
views
is it possible to extract all the exome information from WGS?
genome sequencing
updated 4.5 years ago by 56k • written 4.5 years ago by ▴ 320
0
votes
0
replies
641
views
How to handle mouse events in PyMOL plugins
PyMOLplugin events PyMOL
4.5 years ago by d.s.molodenskiy • 0
0
votes
0
replies
630
views
is the absolute value of `plink2.eigenvec.var` from `plink2 --pca biallelic-var-wts approx` a measure of how much each SNP drives PCS?
plink
4.5 years ago by curious ▴ 890
1
vote
1
reply
2.4k
views
Autodock parse error
autodockautodock_vina
updated 4.5 years ago by ▴ 940 • written 4.5 years ago by • 0
2
votes
3
replies
1.2k
views
Gene Expression
python protein
updated 4.5 years ago by 89k • written 4.5 years ago by • 0
4
votes
5
replies
6.7k
views
VariantsToTable in GATK does not produce the table of all SNPs in the vcf file
GATK
updated 4.5 years ago by • 0 • written 7.1 years ago by ▴ 200
4
votes
2
replies
2.6k
views
htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 92283: Duplicate allele added to VariantContext: C, …
VariantsToTable vcf gatk
4.5 years ago by DareDevil ★ 4.4k
6
votes
3
replies
1.4k
views
Illumina Terminology Clarification
genomics
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 70
0
votes
0
replies
950
views
Job: Cancer Bioinformatician @ University of East Anglia - Norwich Medical School UK
uk cancer postdoc
4.5 years ago by dan.brewer ▴ 120
0
votes
2
replies
3.1k
views
FindIntegrationAnchors returs 0 anchor after filtering
seurat dataintegration FindIntegrationAnchors
4.5 years ago by mbk0asis ▴ 700
0
votes
5
replies
2.4k
views
How to convert physical position to genetic position given 1cM = 1Mb?
IBDLD geneticmap
updated 4.5 years ago by 166k • written 4.5 years ago by ▴ 130
0
votes
7
replies
2.3k
views
I have multiple read count files in txt format, I don't know how to merge them all in a single file
rnaseqR
4.5 years ago by rishav513 ▴ 30
0
votes
0
replies
641
views
Single end or paired end LP WGS
alignment mapping sequencing genomics
4.5 years ago by am ▴ 70
12
votes
14
replies
11k
views
STAR alignment command.
RNA-Seq alignment sequence assembly rna-seq
updated 4.5 years ago by ★ 4.4k • written 7.2 years ago by ▴ 40
5
votes
6
replies
3.9k
views
noisy chip-seq peaks
deeptools macs2 chip-seq peaks igv
updated 4.5 years ago by ★ 19k • written 4.5 years ago by • 0
1
vote
2
replies
2.2k
views
Select one variant from multiple in ALT in VCF file
VCF Filter multiplevariants WGS
updated 4.5 years ago by 9.8k • written 4.5 years ago by ▴ 20
3
votes
1
reply
1.1k
views
RNA-seq stranded protocol
RNA-seq
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 20
2
votes
2
replies
2.7k
views
Visualizing overlap between gene sets in R using circos plots
plot multiplegenesets gene circos R
updated 3.6 years ago by • 0 • written 4.5 years ago by ▴ 130
1
vote
2
replies
1.0k
views
I need to retrieve the genomic locations of all genes in the given read count matrix
RNAseq annotation TEffectR r
4.5 years ago by pavelasquezv ▴ 50
2
votes
4
replies
2.2k
views
A simple question about UCSC genome browser
genome
updated 4.5 years ago by 36k • written 4.5 years ago by • 0
1
vote
14
replies
3.3k
views
need help with bwa
sequence
4.5 years ago by Cony Lab • 0
0
votes
0
replies
851
views
Artificially high rho outputs from LDHat
rho VCF LDHat popgen
4.5 years ago by timothy.delory ▴ 20
61
votes
16
replies
11k
views
14 follow
Forum: Rust or C++, what to learn after Go for high-performance bioinformatics tools?
library
updated 2.7 years ago by ★ 1.3k • written 4.9 years ago by 8.7k
2
votes
3
replies
3.7k
views
featureCounts - ERROR: failed to find the gene identifier attribute in the 9th column of the provided GTF file
genome annotation database alignment
updated 4.5 years ago by 21k • written 4.5 years ago by ▴ 50
0
votes
0
replies
614
views
Need help with BRIG (blank spaces)
genome gene alignment blast
4.5 years ago by Софья • 0
2
votes
1
reply
1.4k
views
ANNOVAR doesn't recognize multiple variants at single locus
SNPs ANNOVAR snpEff SNVs
updated 4.5 years ago by ▴ 290 • written 4.5 years ago by ▴ 30
0
votes
4
replies
3.0k
views
SRAToolKits Trouble
general
updated 4.5 years ago by 103k • written 4.5 years ago by ▴ 10
0
votes
12
replies
2.8k
views
Write free text comment with @CO in BAM file
BAM hstjdk java
4.5 years ago by mhasa006 ▴ 70
2
votes
0
replies
908
views
Tool: New Tuberculosis in 3D Interactive Viewer
tuberculosis viewer 3D
4.5 years ago by karlynn.noble ▴ 60
0
votes
1
reply
1.3k
views
suggestion for any contamination identifier& filter tool for genome assembly
genome
updated 4.5 years ago by ★ 1.8k • written 4.5 years ago by ▴ 20
0
votes
1
reply
1.0k
views
Identification of plastid derived sequences
workflow
updated 4.5 years ago by ★ 1.8k • written 4.5 years ago by ▴ 90
0
votes
4
replies
1.6k
views
IGV run batch
IGV
4.5 years ago by beaferbl ▴ 10
1
vote
5
replies
2.1k
views
Sortmerna: index fna file from ncbi
sortmerna index rrna
updated 4.5 years ago by 153k • written 4.5 years ago by • 0
1
vote
1
reply
2.2k
views
Stringtie de novo VS reference guided (-G)
reference-guided denovo stringtie RNA-seq
updated 4.5 years ago by 103k • written 4.5 years ago by • 0
1
vote
2
replies
1.1k
views
how to align sequences in multifasta
alignment
updated 4.5 years ago by 153k • written 4.5 years ago by ▴ 60
5
votes
5
replies
2.4k
views
How can I create a count matrix?
dna workflow genome database gene
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 50
2
votes
2
replies
1.3k
views
Installing SRA Tool Kits
general programming
4.5 years ago by hoffmavl1 ▴ 10
2
votes
6
replies
2.2k
views
How to find orthologus sequences between the different species of non-model organisms?
RNA-Seq Transcript Assembly ORF
4.5 years ago by sunnykevin97 ▴ 1000
3
votes
2
replies
1.0k
views
how to keep only the optimal solution in the multi-map read？
alignment mapping
4.5 years ago by minghuiguo448 • 0
9
votes
5
replies
18k
views
Is Human_G1K_V37.Fasta Hg19?
hg
updated 4.5 years ago by ▴ 290 • written 13.9 years ago by ★ 1.7k
2
votes
2
replies
1.5k
views
How to predict GC-Content percentage of a fasta file?
fasta python3 perl python genome
updated 4.5 years ago by 9.3k • written 4.5 years ago by ▴ 120
0
votes
1
reply
1.5k
views
freebayes 'terminate called after throwing an instance of 'std::out_of_range' error
std::out_of_range freebayes error
updated 4.5 years ago by 166k • written 4.5 years ago by • 0
2
votes
3
replies
1.7k
views
any pipeline for small non coding RNA analysis from total RNA-seq
lhpRNA RNA-seq snRNA pipeline
4.5 years ago by lkianmehr ▴ 100
0
votes
0
replies
621
views
How to find trusted healthy control data for childhood disorders
RNA-seq Rarediseases Peripheralblood
4.5 years ago by nkabo ▴ 80
121,908 results • Page 686 of 2439
Recent Votes
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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