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121,820 results • Page 579 of 2437
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723
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What is the difference between GERP S and GERP N?
annotation GERP pathogenic genomics
updated 3.6 years ago by ▴ 350 • written 4.0 years ago by ▴ 20
0
votes
1
reply
1.3k
views
Pan-genome visualization similar to anvio?
analysis pangenome
updated 4.0 years ago by 3.9k • written 4.0 years ago by ▴ 60
5
votes
1
reply
1.5k
views
What does samtools mean by 'orientation' when marking duplicates?
read_orientation samtools htslib
updated 4.0 years ago by ▴ 390 • written 4.1 years ago by ▴ 180
0
votes
4
replies
2.0k
views
Rare variant association analysis (SKAT-O) - Power calculation
association analysis SKAT-O . Genetics
4.0 years ago by Alexandros.Frydas ▴ 30
0
votes
0
replies
588
views
Using UnifiedGenotyper on single chromosome without coordinates
GATK
4.0 years ago by shpak.max ▴ 60
3
votes
9
replies
3.7k
views
Filter DGElist object: keep only genes expressed in sample at the same time as a particular gene of interest
edger RNA-seq dgelist R
4.0 years ago by Ondina ▴ 100
1
vote
1
reply
898
views
Could it happen that a cwl created in a different editor is not correctly parsed in rabix composer?
rabix cwl
updated 4.0 years ago by 153k • written 4.0 years ago by • 0
7
votes
9
replies
7.4k
views
Merge contigs in fasta file
fasta merge contigs
updated 4.0 years ago by ▴ 10 • written 6.3 years ago by ▴ 350
1
vote
2
replies
1.8k
views
Remote blast query limit
remote blast
4.0 years ago by timothy.kirkwood ▴ 140
1
vote
1
reply
832
views
Cleaning Blast results
codes BLASTP multiple scripts hits
updated 4.0 years ago by 15k • written 4.0 years ago by • 0
0
votes
0
replies
1.8k
views
Job: We are looking for bioinformaticians for collaboration
startup bioinformaticians
updated 2.2 years ago by 45k • written 4.0 years ago by • 0
0
votes
2
replies
1.0k
views
fetch out common/conserved genes from a bunch of bacteria species
common analysis genes comparative
4.0 years ago by zhangdengwei ▴ 210
0
votes
6
replies
3.6k
views
Transcripts mapping using Salmon
Salmon mRNA-seq RNA-seq total
4.0 years ago by g.wang2 ▴ 10
1
vote
1
reply
1.7k
views
SCENIC-openloom not working
sc-rna SCENIC sequencing
updated 23 months ago by • 0 • written 4.0 years ago by ▴ 10
1
vote
6
replies
3.0k
views
Use of GenotypeGVCFs in population genetic studies
WGS Introgression GenotypeGVCFs ADMIXTURE GATK
updated 4.0 years ago by ★ 1.2k • written 4.0 years ago by ▴ 150
1
vote
4
replies
1.4k
views
Cutoff value for shrunken logFC
deseq
updated 4.0 years ago by 89k • written 4.0 years ago by ▴ 20
1
vote
1
reply
2.1k
views
Download TCGA and GTEX data from Xena toilHub for (full genome but for 1 cancer/tissue type)
GTEX UCSCXenaTools TCGA RNA-seq Xena
updated 4.0 years ago by ★ 7.6k • written 4.0 years ago by ▴ 20
0
votes
0
replies
760
views
Community detection protocol and failed gene enrichment
igraph detection community
4.0 years ago by k0stasmp ▴ 10
2
votes
3
replies
2.4k
views
DESeq2 Not full Rank - Age & Medication
medication DESeq2 age rank
updated 4.0 years ago by 105k • written 4.0 years ago by ▴ 40
2
votes
3
replies
2.7k
views
Racon command line with paired-ends Illumina reads
Illumina Racon
updated 23 months ago by 45k • written 4.0 years ago by ▴ 170
1
vote
4
replies
1.3k
views
Determining LOC coordinate from GFF3 start column
GFF3
4.0 years ago by Simon • 0
1
vote
2
replies
1.4k
views
Polygenic Risk Score Plot
Risk Plink Polygenic PRS Score
4.0 years ago by Muhammad ▴ 10
2
votes
1
reply
1.0k
views
Retrieving sequences and Blast them
blast
updated 4.0 years ago by 8.8k • written 4.0 years ago by ▴ 440
1
vote
2
replies
1.1k
views
Specifications for annotation names or symbols?
specification annotation
4.0 years ago by Alex Reynolds 36k
0
votes
1
reply
1.1k
views
DESeq2
DEGs
updated 4.0 years ago by ▴ 320 • written 4.0 years ago by • 0
4
votes
9
replies
4.5k
views
Need help to remove NA values from data frame
DeSEQ2 R
updated 3.9 years ago by ▴ 590 • written 4.0 years ago by ▴ 140
2
votes
2
replies
1.8k
views
Merging .gam files
vg gam
updated 4.0 years ago by • 0 • written 5.3 years ago by ▴ 30
4
votes
4
replies
2.9k
views
Good or bad idea to annotate with newer genome build?
array methylation beadchip build annotation
4.0 years ago by Pratik ★ 1.1k
3
votes
9
replies
3.4k
views
Fasta.fai file error
bedtools
updated 4.0 years ago by 3.1k • written 4.0 years ago by • 0
0
votes
0
replies
829
views
How to merge Bulk ATAC-SEQ with scATAC-SEQ result?
atac scATAC
4.0 years ago by ahmad mousavi ▴ 800
1
vote
1
reply
1.4k
views
RRBS data analysis using Bismark and methylkit
RRBS methylkit Bismark WGBS
updated 4.0 years ago by ★ 3.1k • written 4.0 years ago by ▴ 550
5
votes
1
reply
2.6k
views
ARACNE-AP output for Viper R package
ARACNE ARACNE-AP Viper
updated 4.0 years ago by ▴ 30 • written 4.2 years ago by ▴ 20
0
votes
0
replies
592
views
Inter-sample variance explained
composition inter-sample single-cell variance clsuter
4.0 years ago by christianhinze • 0
2
votes
1
reply
1.2k
views
R package for structural variation representation ?
structural variation mummer
updated 4.0 years ago by 4.1k • written 4.0 years ago by ▴ 690
0
votes
0
replies
1.4k
views
Apply a batch effect with "combatseq" in wgcna
deseq2 R batch combatseq wgcna
updated 4.0 years ago by 13k • written 4.0 years ago by • 0
3
votes
6
replies
4.3k
views
gffread error
gtf gff gffread
4.0 years ago by rhksgudbc • 0
0
votes
2
replies
1.3k
views
Removing headlines in fasta file in python
fasta python
updated 2.6 years ago by 45k • written 4.0 years ago by • 0
0
votes
2
replies
3.0k
views
Remove PolyA 3'End with cutadapt
sequencing
4.0 years ago by GiV17 ▴ 50
7
votes
1
reply
4.3k
views
HTseq doesn't support Multi-Threading ?
htseq-count htseq thread multithread count
updated 4.0 years ago by 56k • written 4.0 years ago by ▴ 20
1
vote
2
replies
958
views
Can the Non strand specify RNAseq data annotate genome?
RNA-Seq
4.0 years ago by yiren ▴ 10
0
votes
4
replies
1.7k
views
How to filter GATK vcf file using other programs
VCF Filtration GATK
4.0 years ago by reza ▴ 300
5
votes
8
replies
2.5k
views
How to make fasta manipulation more efficient
fasta sequence
4.0 years ago by c_u ▴ 530
0
votes
0
replies
754
views
Separate vcf file creation for matched tumor-normal samples
vcf
4.0 years ago by Gene_MMP8 ▴ 240
1
vote
1
reply
722
views
Clarification on transcripts
Transcripts genes
updated 4.0 years ago by 89k • written 4.0 years ago by • 0
1
vote
2
replies
1.3k
views
where do I find transcript_biotype
refseq biotype transcript
updated 4.0 years ago by • 0 • written 4.0 years ago by • 0
3
votes
5
replies
2.2k
views
Commandline BLAST - errors?
line BLAST RNA-seq command
updated 4.0 years ago by ★ 1.1k • written 4.0 years ago by • 0
0
votes
0
replies
614
views
What is meant by transcriptional changes executed by the cell over a time period?
single-cell rna dna transcriptome-regulation gene
4.0 years ago by Deepak • 0
1
vote
7
replies
2.7k
views
6 follow
genBlastA output file .gblast error
genome sequence software error
updated 2.4 years ago by ▴ 30 • written 4.8 years ago by • 0
5
votes
7
replies
2.4k
views
Genomic landscape of Neisseria gonorrhoeae wild-type strain whole genome schematic.
Figures Neisseria_gonorrhoeae regions whole_genome Strain
updated 4.0 years ago by 153k • written 4.0 years ago by ▴ 100
5
votes
6
replies
2.2k
views
Can HMMs detect partial proteins sequences?
metagenomics HMM
4.0 years ago by Rui ▴ 50
121,820 results • Page 579 of 2437
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Recent Replies
Answer: High percentage of intronic/intergenic reads in RNA-seq by Jorge • 0
I know this is an old post, but I experienced the same issue using rRNA depletion kit and found this paper https://www.nature.com/articles…
Comment: Add reference genomes as an outgroup to a phylogenetic tree by Michael 56k
Traditionally, mtDNA sequences have been used for this species. Several rounds of whole-genome duplication and autotetraploidy make whole n…
Comment: Add reference genomes as an outgroup to a phylogenetic tree by Michael 56k
That's interesting from a Norwegian perspective. You also may find [SalmoBase][1] useful. [1]: https://salmobase.org/#About
Comment: deeparg-takes-too-many-threads by Dave Carlson ★ 2.1k
I'm not particularly familiar with Concoct, but from glancing [at the code][1], it does appear to use OpenMP, so I would expect that setti…
Comment: Learning Bioinformatics doing Projects by Pierre Lindenbaum 166k
This post does not fit the theme of this forum.
Comment: Learning Bioinformatics doing Projects by jared.andrews07 ★ 19k
There is nothing stopping you from doing those things. This is not a question.
Comment: deeparg-takes-too-many-threads by GenoMax 153k
Related past thread for reference: https://www.biostars.org/p/9613794/ , in case you know about the programs mentioned.
Comment: best practice for diploid variant calling by cmdcolin ★ 4.3k
that is quite a cool experiment. I am not actually sure of the best approach (sorry to disappoint). I think that if you look up "phased ass…
Comment: Add reference genomes as an outgroup to a phylogenetic tree by dthorbur ★ 3.1k
I'm sure there are phylogenetics papers out there comparing species within this genus - a quick google seems to suggest there is up to 15M …
Comment: deeparg-takes-too-many-threads by Dave Carlson ★ 2.1k
Note that vsearch uses pthreads, *not* OpenMP, for multithreading. Therefore setting OpenMP environment variables (e.g., `OMP_NUM_THREADS`…
Comment: Add reference genomes as an outgroup to a phylogenetic tree by Álvaro • 0
Thank you I will try this!
Comment: Add reference genomes as an outgroup to a phylogenetic tree by Álvaro • 0
I'm working with Salmo trutta and wanted to use Salmo salar as an outgroup. I have whole-genome .fastq data of the trout samples. Sorry, I'…
Comment: deeparg-takes-too-many-threads by GenoMax 153k
> I am running it withing a screen session If you are using `screen` then you may need to set the variables in a different way. Try to se…
Comment: deeparg-takes-too-many-threads by shevch2009 ▴ 20
Thanks, I will look for another tools. Yes, I am running it withing a screen session.
Comment: deeparg-takes-too-many-threads by GenoMax 153k
If the program is not respecting limits you are setting then you may need to dive into code to see why that is happening. It may or may not…
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