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Showing top results for tag: sequence • reset
0
votes
1
reply
1.4k
views
Problems with using Phobius
Phobius fasta sequence
updated 10 days ago by 44k • written 4.7 years ago by • 0
5
votes
2
replies
273
views
Query regarding the ST visulization
Visualization Circos Sequence
7 weeks ago by Jaykumar ▴ 50
15
votes
4
replies
407
views
How to perform reciprocal best hit (RBH) when there are multiple versions of a protein sequence
reciprocal.best.hit protein sequence RBH blast
updated 7 weeks ago by 4.3k • written 7 weeks ago by ★ 1.3k
0
votes
1
reply
339
views
Stranded cDNA libraries and genome mapping
cDNA sequence strand
updated 12 weeks ago by ★ 1.3k • written 12 weeks ago by ▴ 10
0
votes
0
replies
209
views
MEME PWM format - what is the meaning of nsites?
motif sequence meme-suite pwm meme
3 months ago by mcsimenc ▴ 20
2
votes
4
replies
1.3k
views
Need to create a small artificial SRA file for unit testing
sequencing sequence
4.6 years ago by Sean McCorkle ▴ 20
0
votes
1
reply
268
views
Manual Assembly and Protein Translation, HELP, assignment revision
sequence university assembly protein genomics
updated 4 months ago by 8.7k • written 4 months ago by ▴ 20
0
votes
0
replies
185
views
Successfully identified and Masked rpeats using RM. What Next?
sequence annotation repeatmasker illumina assembly
5 months ago by Vijith ▴ 40
0
votes
3
replies
945
views
Why cd-hit-est not work when sequence identity threshold<0.95？
genome cluster sequence
updated 5 months ago by • 0 • written 2.2 years ago by • 0
3
votes
3
replies
463
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide Genomic Sequence Uniprot Proteins
updated 5 months ago by 145k • written 5 months ago by ▴ 50
0
votes
4
replies
801
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
5 months ago by Kai Xin • 0
2
votes
11
replies
1.3k
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 5 months ago by ★ 1.3k • written 5 months ago by • 0
0
votes
1
reply
286
views
Geneious Prime (Consense Sequence)
Consense Sequence
updated 5 months ago by 145k • written 5 months ago by • 0
0
votes
2
replies
382
views
BLASTP short sequences (<20aa) - interpreting results
blast sequence blastp alignment
5 months ago by neish • 0
2
votes
3
replies
916
views
Should I use Dfam or a custom repetitve elements library (from PlantRep) as a repeat database; using RepeatMasker in a Linux machine?
genome sequence repeatmasker blast
updated 6 months ago by ▴ 290 • written 6 months ago by ▴ 40
0
votes
16
replies
1.5k
views
What is the sequence origin in human plasma?
human sequence cfDNA
5 months ago by biwdpang • 0
3
votes
5
replies
825
views
Searching for gene in multiple genomes
gene genome alignment sequence
updated 6 months ago by ★ 2.1k • written 6 months ago by • 0
0
votes
1
reply
333
views
Extract Umi sequence to readname
Sequence FgBio UMI
updated 6 months ago by 145k • written 6 months ago by • 0
3
votes
4
replies
768
views
Why many organisms even though they possess mitochondrial DNA (mtDNA), it is not typically represented by chromosomes labeled as "mtDNA"?
genome mtDNA reference-genome sequence
6 months ago by George X. • 0
4
votes
3
replies
2.6k
views
How to deal with gaps during translation with biopython
sequence
updated 7 months ago by ▴ 10 • written 5.4 years ago by ▴ 110
4
votes
5
replies
1.1k
views
Any ways of extracting and filtering read sequences from cram files with samtools?
samtools cram reads sequence
6 months ago by sacryt • 0
0
votes
1
reply
405
views
How to obtain fine-scale classification from Kraken2
Kraken2 sequence metagenome assembly
updated 7 months ago by ★ 3.0k • written 7 months ago by ▴ 260
1
vote
6
replies
4.8k
views
Mouse to Human Protein Alignment Maps
alignment sequence mouse
updated 7 months ago by ▴ 30 • written 8.0 years ago by ▴ 600
4
votes
9
replies
1.1k
views
How to accelerate BLASTING
NCBI Blast sequence
7 months ago by anikcropscience ▴ 260
0
votes
1
reply
2.6k
views
Impact of k-mer length for kraken2 database
sequence
updated 7 months ago by • 0 • written 5.4 years ago by • 0
0
votes
0
replies
364
views
Sequence alignment similarity score including weakly conserved groups
alignment protein sequence
updated 7 months ago by 44k • written 7 months ago by ▴ 80
2
votes
5
replies
856
views
Sequence alignment matrix
alignment protein sequence
updated 7 months ago by ★ 28k • written 7 months ago by ▴ 80
0
votes
1
reply
282
views
coding sequence
biology sequence molecular coding gene
updated 8 months ago by 164k • written 8 months ago by • 0
8
votes
7
replies
1.3k
views
6 follow
Why is local BLAST so slow? (yet another one of these questions)
blast ncbi sequence
8 months ago by mykle hoban ▴ 40
1
vote
0
replies
280
views
Tool: BIRCH3.90 - BioLegato, Apple Silicon, Updates
genomics sequence transcriptomics
8 months ago by brian.fristensky ▴ 460
22
votes
7
replies
17k
views
6 follow
GFA to Fasta file
sequence
updated 8 months ago by ▴ 40 • written 8.8 years ago by ▴ 90
0
votes
2
replies
407
views
EBI UniParc vs NCBI NR protein databases
BLAST proteins sequence
8 months ago by cdsouthan ★ 1.9k
0
votes
2
replies
1.1k
views
How to define the density (or something else) of B in the sequence, considering the number of B in the sequence and the distance between B
density sequence
updated 9 months ago by 20k • written 9 months ago by • 0
0
votes
20
replies
2.1k
views
How can I obtain the DNA sequences of each CDS for several genbank files?
genbank DNA sequence
9 months ago by Raphaëlle • 0
4
votes
12
replies
7.3k
views
Extract fasta sequence from gff3 file
sequence
updated 9 months ago by ▴ 10 • written 3.6 years ago by ▴ 10
9
votes
15
replies
8.3k
views
Efficient way of calculating the number of mismatches between two sets of sequences please?
alignment genome sequence
updated 2.6 years ago by 44k • written 9.8 years ago by ▴ 360
2
votes
3
replies
942
views
Generate a sequence of specific length with a list of motifs and intersperse with spacers
python R perl motif sequence
updated 10 months ago by • 0 • written 3.3 years ago by ▴ 30
2
votes
7
replies
15k
views
How too choose outgroup for rooting a phylogenetic tree?
phylogeny sequence alignment
updated 10 months ago by ▴ 60 • written 9.5 years ago by ★ 2.8k
1
vote
3
replies
592
views
DNA/RNA Sequence Alignment
dna rna alignment sequence
updated 10 months ago by ★ 28k • written 10 months ago by • 0
0
votes
1
reply
548
views
how to create a consensus sequence from different assemblies
consensus sequence
updated 10 months ago by 20k • written 10 months ago by ▴ 10
0
votes
3
replies
6.2k
views
Parsing Pdb file using Biopython parser: How to get all atoms instead of duplicates?
sequence software error assembly biopython
updated 10 months ago by ▴ 20 • written 5.1 years ago by • 0
0
votes
0
replies
383
views
Blog: Uncovering the Genetic Basis of Rare and Complex Diseases through Whole Genome Sequencing (WGS)
genome WGS illumina GWAS sequence
10 months ago by Novogene ▴ 460
25
votes
4
replies
42k
views
bcftools compressing and indexing vcf files
sequence bcftools vcf index
updated 10 months ago by 145k • written 6.1 years ago by ▴ 280
3
votes
2
replies
599
views
Protein Sequence from Entrez by Taxonomic_ID: Very slow
Efetch entrez python protein sequence
11 months ago by The ▴ 180
5
votes
7
replies
3.4k
views
8 follow
bwa mem -T (alignment score) not doing anything
SNP genome sequence
updated 11 months ago by 101k • written 6.3 years ago by ▴ 10
5
votes
6
replies
4.9k
views
How To Find The Enriched Repeat Elements Between Two Sequences
repeats sequence enrichment
updated 11 months ago by • 0 • written 12.6 years ago by ▴ 180
2
votes
4
replies
4.6k
views
Is there a way to use CNVkit without a reference from normal samples?
sequence CNVkit
updated 12 months ago by ★ 3.6k • written 6.5 years ago by • 0
5
votes
7
replies
1.0k
views
How the first sequencing template removed in pair end sequencing
NGS RNA-seq WGS sequence
updated 12 months ago by 145k • written 12 months ago by ▴ 110
38
votes
25
replies
9.8k
views
13 follow
FASTA file of fixed length
sequence fasta
updated 12 months ago by 44k • written 8.5 years ago by ▴ 250
2
votes
3
replies
1.1k
views
What is the fastest nucleotide sequence alignment search tool for 100mer queries versus a 2G database for nearly similar matches
alignment read nucleotide aligner sequence
updated 12 months ago by 145k • written 12 months ago by ▴ 40
50 results • Page 1 of 1
Recent Votes
Answer: Converting bam to sam using htslib C++ api
Answer: How to compile Multiz
Comment: How to compile Multiz
Alignment tool for very short reads (25bp)
Comment: How to compile Multiz
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
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Recent Replies
Comment: Sankey + dot plot by zx8754 12k
What is the problem, where is the code you are trying? Provide code, example data, expected output.
Answer: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Michael 55k
Something went wrong during star alignments of samples OE1_2, OE1_3, and OE_NC_1. The obvious place to look for the reason is in the Star l…
Comment: How to compile Multiz by Pierre Lindenbaum 164k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: How to compile Multiz by Santex • 0
I'm sorry. I post a new question.
Comment: NeuronChat: identifyCommunicationPatterns_Neuron() error by sooni ▴ 20
I solved the problem by installing `NMF` package.
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
Can you check using `featureCounts` to make sure things look reasonable with alignments? You could also use `salmon` to do transcript quant…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
Since we don't have access to your data we can't comment. Check the integrity of your input data files. Validate the files if you are not s…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
https://www.biostars.org/u/145859/ : Use `ADD REPLY/ADD COMMENT` to add additional information to existing threads. `ADD YOUR ANSWER` is me…
Comment: How to compile Multiz by GenoMax 145k
Please do not ask questions unrelated to the original post in this thread. Post a new question.
Comment: How to compile Multiz by Santex • 0
I could install multiz from it! Thank you very much. Please help me out with the problem below. I run multiz like below. (myenv) tak…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
One of them looks okay, but I don't quite believe it. ```R > table(df$`intermediate_data.OE1_1_.genes.results`==0) FALSE TRUE 21200 2…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
It seems that the files that generated the results also have significant issues. Except for one sample, all other samples only have over 20…
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
Their .fq files all look similar, should I rerun these programs?
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by GenoMax 145k
> Cannot open intermediate_data/OE_NC_2_.temp/OE_NC_2__alignable_1.fq! It may not exist. Looks like you are missing some files. BTW this …
Comment: I have encountered some bugs in transcriptome analysis using STAR and RSEM. by Pallondyle • 0
The most torturous thing is that some groups did indeed generate results. ``` ls intermediate_data KO1_1_.stat KO1_3_.isoforms…
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