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Showing top results for tag: Kmer • reset
2
votes
6
replies
1.3k
views
Mapping all 32-mers within Hamming Distance = 3
hamming alignment kmer ngs short
updated 23 days ago by ▴ 30 • written 23 months ago by ▴ 10
5
votes
3
replies
541
views
How to represent arbitrarily length kmer?
kmer
9 weeks ago by dwpeng ▴ 100
4
votes
9
replies
790
views
Kallisto - Effect of Kmer size on quantification?
Kallisto single-overhang Kmer RNA-seq length
3 months ago by jayeshkumarsundaram • 0
0
votes
1
reply
277
views
Fastqc: kmer-content failed
fastqc kmer
updated 4 months ago by 44k • written 4 months ago by • 0
1
vote
1
reply
313
views
Failed kmer content
kmer illumina ngs
updated 6 months ago by 44k • written 6 months ago by • 0
0
votes
4
replies
632
views
kmer analysis for genome size estimation
kmer merqury allotetraploid pacbio hifiasm
7 months ago by rj.rezwan ▴ 10
0
votes
0
replies
191
views
Difference between reading concatenated PE reads into jellyfish and merging paired end .jf outputs independently
Jellyfish Kmer GenomeScope
7 months ago by joshua.j.wright ▴ 10
1
vote
0
replies
336
views
Tool: HFKReads, an ultra-fast and efficient tool for high frequency kmer sequencing reads extraction
kmer organelle metagenomic assembly
8 months ago by Huiyang ▴ 190
2
votes
5
replies
903
views
Jellyfish & Paired end reads
Jellyfish genome-assembly kmer
updated 8 months ago by 4.7k • written 8 months ago by ▴ 10
7
votes
3
replies
525
views
Should you remove PCR duplicates for kmer counting?
kmer dedup duplicates
updated 8 months ago by 4.7k • written 8 months ago by ▴ 40
0
votes
0
replies
318
views
jellyfish histo is empty
jellyfish kmer fastq
11 months ago by m.t.lorenc • 0
0
votes
3
replies
739
views
Jellyfish problem with Failed to open input file 'reads.jf'
jellyfish kmer fastq
11 months ago by m.t.lorenc • 0
4
votes
4
replies
1.0k
views
Best way to use k-mers as a predictor in my neural network
convolutional-neural-network kmer
updated 12 months ago by 20k • written 12 months ago by ▴ 30
0
votes
2
replies
594
views
Visualize where kmers are on a reference genome
kmer visualize
updated 13 months ago by 35k • written 13 months ago by • 0
0
votes
0
replies
378
views
jellyfish options
kmer jellyfish
17 months ago by Tele • 0
1
vote
2
replies
822
views
Help with understanding BBduk's behavior
BBduk kmer
17 months ago by Dave Carlson ★ 1.9k
3
votes
3
replies
3.4k
views
python function to kmer with windown size
python kmer biopython fasta
updated 20 months ago by • 0 • written 4.8 years ago by ▴ 280
1
vote
1
reply
603
views
Why does `bowtie` only find perfect matches even when specifying mismatches? (ie. `-n 3`)
ngs alignment bowtie kmer
updated 23 months ago by 14k • written 23 months ago by ▴ 10
1
vote
1
reply
798
views
Merge Trinity assembly
de assembly novo kmer trinity
updated 2.2 years ago by ★ 1.4k • written 2.2 years ago by • 0
0
votes
1
reply
589
views
Interpreting Tallymer search output
tallymer kmer
2.5 years ago by jmartin • 0
0
votes
1
reply
494
views
minimap2 without kmer filter crashes
alignment minimap2 kmer
updated 2.5 years ago by ▴ 20 • written 2.5 years ago by • 0
4
votes
8
replies
1.2k
views
Extract origin location and name kmers from source sequence
kmer
2.7 years ago by vivek37373 • 0
1
vote
2
replies
1.1k
views
How to decide Kmer in Spades?
Fastq Spades WGS Kmer
2.7 years ago by bioinfo223 ▴ 10
0
votes
1
reply
748
views
Does it necessary to use both forward and reverse fastq input files in kmergnie?
kmer
updated 2.8 years ago by ★ 1.4k • written 2.8 years ago by • 0
3
votes
6
replies
1.8k
views
Create smallest set of k-mers using degenerate bases
kmer degenerate
updated 2.9 years ago by 35k • written 3.0 years ago by • 0
0
votes
1
reply
770
views
How to use a protein alignment fasta file when using the function cluster of Kmer package
arrays kmer AAbin
updated 3.1 years ago by 11k • written 3.1 years ago by • 0
1
vote
2
replies
1.1k
views
Tool: krust: a k-mer counter in Rust using the rust-bio and rayon crates
Rust kmer-counting fasta kmer
updated 3.2 years ago by 101k • written 3.2 years ago by ▴ 10
0
votes
0
replies
513
views
Falco indicates that Kmer content FAIL, but there are no Kmer content in fastqc_data.txt
kmer falco
3.2 years ago by kamanovae ▴ 100
0
votes
0
replies
606
views
What are the minimal contig length and kmer coverage below which I should drop some contigs in viral metagenomics study after assembly with Spades?
Kmer Length Contigs coverage Metagenomics
3.3 years ago by bioAddict • 0
1
vote
1
reply
2.5k
views
k-mer distribution to estimate the heterozygosity of my assembly
kmer Assembly pacbio purge_dups
updated 3.4 years ago by ▴ 220 • written 3.9 years ago by ▴ 310
0
votes
0
replies
700
views
Canu possibly idling in the "meryl" step
canu meryl assembly genomics kmer
3.6 years ago by Matteo Schiavinato ★ 3.6k
2
votes
3
replies
1.6k
views
Short sequence alignment using Minimap2
assembly minimap2 kmer gRNA pacbio
updated 3.6 years ago by 146k • written 3.7 years ago by ▴ 10
5
votes
2
replies
4.9k
views
From .csv file to fasta
fasta python genome Assembly kmer
3.8 years ago by Sbrillo ▴ 10
1
vote
0
replies
910
views
Kmer analysis of large amino acid datasets
sequencing kmer
3.8 years ago by eeveeody • 0
0
votes
8
replies
1.9k
views
get error in kmer counting in python 3
kmer python DNA FASTA
updated 3.9 years ago by 44k • written 3.9 years ago by ▴ 140
5
votes
3
replies
1.3k
views
How to determine coverage cutoffs in k-mer distribution
kmer distribution kmer Assembly
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 310
3
votes
4
replies
1.4k
views
what's the best Kmer should be set when assembling bacteria genome
genome assembly Kmer
4.2 years ago by zhangdengwei ▴ 210
1
vote
1
reply
931
views
DSK GATB installation Windows
Assembly kmer DSK WINDOWS
4.2 years ago by mimarcelape • 0
2
votes
1
reply
2.0k
views
How can you determine ploidy of a genome?
ploidy kmer genomescope jellyfish
updated 4.2 years ago by 35k • written 4.2 years ago by ▴ 170
0
votes
1
reply
1.0k
views
BBnorm not outputting txt files when trying to determine ploidy on pb fastq.gz reads
kmer khist bbnorm bbmap ploidy
updated 4.3 years ago by 146k • written 4.3 years ago by ▴ 170
17
votes
13
replies
3.1k
views
8 follow
Finding 16 mer not present in GRCh38
kmer genome
updated 15 months ago by ▴ 160 • written 5.9 years ago by ▴ 60
26
votes
8
replies
5.4k
views
6 follow
Blog: Fast kmer reverse complement code using bit tricks
kmer code reverse-complement gatb
updated 2.8 years ago by 44k • written 10.1 years ago by ★ 1.5k
1
vote
1
reply
1.9k
views
kmer counting for heterozygosity estimation
jellyfish kmer heterozygosity genome assembly
updated 4.8 years ago by ▴ 380 • written 4.8 years ago by ▴ 80
4
votes
7
replies
6.3k
views
best kmer for genome size estimation
genome kmer
updated 4.9 years ago by ▴ 470 • written 6.9 years ago by ▴ 110
4
votes
7
replies
3.0k
views
jellyfish kmer counting discrepancy
kmer count genome RNA-Seq jellyfish
updated 5.1 years ago by 101k • written 5.1 years ago by • 0
0
votes
0
replies
2.0k
views
Sequence read (id) specific kmer frequency calculation
kmer reads sequence metagenome
updated 2.2 years ago by 44k • written 8.9 years ago by • 0
0
votes
0
replies
922
views
Meaning of these k-mer diagrams
assembly alignment kmer jellyfish
5.2 years ago by macielrodriguez2 ▴ 50
2
votes
13
replies
5.5k
views
BBTools/BBMap/BBSuite's sketch.sh and sendsketch.sh are inconsistent
bbmap kmer sketch bbtools bbsuite
5.3 years ago by O.rka ▴ 740
0
votes
2
replies
1.3k
views
Explanation for kmer enrichment after skewer trimming of the RNA-seq reads
skewer fastqc kmer
updated 5.3 years ago by • 0 • written 5.7 years ago by • 0
1
vote
7
replies
2.0k
views
how can I translate my GenomeScope results? Is it make sense?
Assembly sequencing assembly genome kmer
5.4 years ago by dongseokkim6662 • 0
50 results • Page 1 of 1
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The Biostar Herald for Friday, November 01, 2024
The Biostar Herald for Friday, November 01, 2024
Clustering and dynamic tree cutting
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How?
Answer: Coverage data for TCGA BAM files
Answer: Coverage data for TCGA BAM files
RNA-Seq vs DNA-Seq variant calling
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Recent Replies
Comment: Are there any preferred trajectory/pseudotime analyses that do not require an ar by Jean-Karim Heriche 27k
Maybe consider seriation/ordination as an alternative.
Comment: dedup STAR transcriptome file using umi_tools by i.sudbery 20k
There are bulk protocols that include UMIs. Lexogen's CORRAL kits for example. Or NEB's NEBNext UMI adaptors.
Answer: dedup STAR transcriptome file using umi_tools by Michael 55k
I am quite sure that you cannot use UMI_tools to deduplicate bulk RNA-seq. The different oligo adapter sequences on each bead introduce UMI…
Answer: dedup STAR transcriptome file using umi_tools by i.sudbery 20k
I don't know if any reason you shouldn't be able to index the bam produced by STAR, although you will need to sort them first.
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by wangziwei0010 ▴ 30
Hi ATpoint, Thank you for your though provoking answer. Big fans! Actually I have some normal cells in each sample, and I found good mixt…
Answer: Differential binding analysis between different TFs by Ming Tommy Tang ★ 4.5k
have you taken a look at csaw? https://bioconductor.org/books/release/csawBook/ also, I am not sure how you can compare different TFs, the…
Comment: R encountering fatal error and quitting the session by Dunois ★ 2.7k
Have you tried running this in a fresh, clean `R` session with no other (unnecessary) packages and data being loaded into memory? How much …
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You most likely have duplicates somewhere in there in the column that is currently serving as index to (I am guessing) the counts DataFrmae…
Comment: What to do with sequences without hits after doing blast against a reference tra by Dunois ★ 2.7k
Expand your search by searching these (two) sequences against other sets of sequences. That said, why does it feel like this is an [XY pro…
Comment: Compare Two Sigle-cell Sample for Differentially Expressed Genes (DEGs). How? by ATpoint 85k
It's confounded. SCtransform is not doing anything in such situations and hatmony operates on a per-cell embeddings level and not per gene …
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
I'm wondering if this could work: `bcftools query -f '[%GT]\n' my.vcf.gz | awk '{ gsub(/\./, ""); print }' | grep -Ev '^(.)\1+$' | wc -l` …
Comment: GISTIC 2.0 parameter change not happening by Ram 44k
You should contact the [GenePattern google group](https://groups.google.com/g/genepattern-help) - that's where you stand a higher chance of…
Comment: find marker using scRNAseq data by allingt • 0
What method are you using to identify markers and does it allow for nested designs?
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
I will look into this. Thank you!
Comment: count number of polymorphic sites among samples in vcf by vaellis • 0
example vcf: ``` CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ind1 ind2 ind3 ind4 chr1 100 . C …
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