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0
votes
2
replies
203
views
How do you get functional/biological role of motifs?
JASPAR
updated 4 days ago by 2.8k • written 5 days ago by ▴ 240
2
votes
8
replies
303
views
How to get names and class information from a list of target IDs from the JASPAR database?
JASPAR
updated 6 days ago by 68k • written 6 days ago by ▴ 240
3
votes
3
replies
360
views
Program to detect cis-regulatory modules for a non model species?
factors transcription
10 weeks ago by DNAngel ▴ 240
4
votes
3
replies
368
views
How do you find transcription factors in a newly sequenced genome?
interproscan factors transcription
updated 3 months ago by ▴ 20 • written 3 months ago by ▴ 240
7
votes
8
replies
408
views
How do you obtain a list of transcription factors from a genome?
question
updated 3 months ago by ▴ 220 • written 3 months ago by ▴ 240
0
votes
6
replies
404
views
Confused about which database to use - nt or nr?
blast
updated 4 months ago by 11k • written 4 months ago by ▴ 240
0
votes
2
replies
367
views
What happened to the SparCC github repository?
sparcc
updated 9 months ago by ★ 1.5k • written 9 months ago by ▴ 240
2
votes
8
replies
2.1k
views
Why does Kraken2 not produce taxon percentages with --report flag?
kraken2
updated 13 months ago by ▴ 80 • written 21 months ago by ▴ 240
0
votes
0
replies
407
views
Can I use DESeq2 to analyze my abundance dataset, which also happens to have a lot of zeros?
deseq2
16 months ago by DNAngel ▴ 240
2
votes
4
replies
870
views
WGCNA, what does it mean if no hub genes are identified?
WGCNA
16 months ago by DNAngel ▴ 240
1
vote
0
replies
369
views
R package for determining best model transformation for a dataset?
R
17 months ago by DNAngel ▴ 240
11
votes
15
replies
1.5k
views
Output of samtools view, what does the third column actually represent?
samtools
updated 17 months ago by 16k • written 17 months ago by ▴ 240
0
votes
0
replies
357
views
How to find out how many reads were used in contig assembly in metaSPADES?
metaspades
17 months ago by DNAngel ▴ 240
1
vote
1
reply
571
views
How do you interpret Tukey's significance when there is no group clustering alone?
Tukey
17 months ago by DNAngel ▴ 240
1
vote
1
reply
689
views
What is the difference between using -max_target_seqs 1 -max_hsps 1 versus just the defaults and then filtering for top hit?
blast
updated 17 months ago by 125k • written 17 months ago by ▴ 240
0
votes
0
replies
304
views
R vegdist does not compute distances for all my sites
vegan vegdist R
updated 17 months ago by 37k • written 17 months ago by ▴ 240
2
votes
1
reply
1.0k
views
What is the recommended contig length to filter?
metaspades
updated 18 months ago by ★ 22k • written 18 months ago by ▴ 240
2
votes
6
replies
670
views
Is there a different names.dmp file in the taxonomy name/id browser?
ncbi
updated 18 months ago by 125k • written 18 months ago by ▴ 240
1
vote
11
replies
1.1k
views
Blast 2.11 not blasting all sequences in a file?
blast
19 months ago by DNAngel ▴ 240
7
votes
12
replies
948
views
7 follow
Why do I lose sequences when converting my bam files into fastq?
fastq bam bamToFastq
updated 19 months ago by 13k • written 19 months ago by ▴ 240
0
votes
0
replies
456
views
Confused about sambamba syntax for unmapped and mapped
sambamba
19 months ago by DNAngel ▴ 240
2
votes
2
replies
476
views
Does spades/metaspades normally having missing nodes?
metaspades spades
19 months ago by DNAngel ▴ 240
3
votes
5
replies
728
views
How to use lapply to extract taxonomic information in my species list?
R
20 months ago by DNAngel ▴ 240
0
votes
2
replies
392
views
How to get domain/kingdom name in a table of taxid in R tidyverse?
R
20 months ago by DNAngel ▴ 240
2
votes
3
replies
1.9k
views
kraken2 unclassified output does not work with paired reads?
Kraken2
updated 20 months ago by 96k • written 20 months ago by ▴ 240
1
vote
1
reply
814
views
Best method to visualize metagenomic data besides krona?
metagenomics krona
updated 20 months ago by 3.1k • written 20 months ago by ▴ 240
3
votes
6
replies
1.4k
views
Bamtools stats and samtools flagstat produce different results and confusing my sambamba output.
sambamba bamtools samtools
20 months ago by DNAngel ▴ 240
0
votes
6
replies
1.4k
views
What do you do with the data processed after running metaspades/spades?
metaspades spades
updated 21 months ago by 3.1k • written 21 months ago by ▴ 240
0
votes
2
replies
561
views
What to do with mapped reads after assembly?
Assembly annotation
24 months ago by DNAngel ▴ 240
0
votes
11
replies
780
views
Error when trying to convert BAM file to FASTQ.
samtools bedtools
24 months ago by DNAngel ▴ 240
0
votes
6
replies
1.1k
views
FastQC Per sequence GC count always fails after trimmomatic?
fastqc trimmomatic
updated 24 months ago by 125k • written 24 months ago by ▴ 240
2
votes
13
replies
4.3k
views
How do you download the nt database for Kraken2?
Kraken2 nt
updated 2.0 years ago by 125k • written 2.0 years ago by ▴ 240
0
votes
6
replies
583
views
Papers/posts on best practises for dealing with Illumina reads?
assembly trimmomatic bwa-mem
updated 2.0 years ago by 68k • written 2.0 years ago by ▴ 240
0
votes
2
replies
437
views
Determining if the number of significant results between two categories is significantly different?
statistics
2.2 years ago by DNAngel ▴ 240
0
votes
0
replies
358
views
How to know if it is missing a gene or assembly error?
BWA Bioinformatics Assembly
2.2 years ago by DNAngel ▴ 240
0
votes
0
replies
420
views
PAML sample size question and variation in results
PAML
2.3 years ago by DNAngel ▴ 240
0
votes
0
replies
778
views
Understanding PAML results between random-sites and clade model C.
PAML
2.3 years ago by DNAngel ▴ 240
2
votes
3
replies
1.3k
views
How to parallelize bwa mem for single-end data within a larger bash script?
bash bwa-mem gnu-parallel
updated 3.3 years ago by 152k • written 3.3 years ago by ▴ 240
2
votes
2
replies
1.4k
views
How do you extract longest transcript from fasta file using length and header IDs?
awk fasta
updated 3.3 years ago by 13k • written 3.3 years ago by ▴ 240
2
votes
1
reply
1.4k
views
How to loop over a directory to set each file as a variable?
bash
3.3 years ago by DNAngel ▴ 240
3
votes
7
replies
965
views
Does Abyss work on single-end Illumina reads only?
Abyss
updated 3.3 years ago by 8.2k • written 3.3 years ago by ▴ 240
4
votes
6
replies
1.4k
views
How do you assemble contigs without using a reference genome?
assembly genome
updated 3.3 years ago by 34k • written 3.3 years ago by ▴ 240
1
vote
6
replies
1.5k
views
What do you do after obtaining sorted bam files?
bwa bam
updated 3.3 years ago by 13k • written 3.3 years ago by ▴ 240
0
votes
0
replies
601
views
How to obtain protein-coding sequences from assembled genome/exome dataset?
PAML bwa
3.3 years ago by DNAngel ▴ 240
0
votes
0
replies
546
views
How to test evolutionary rates for each species in a gene alignment?
evolutionary rate R
3.5 years ago by DNAngel ▴ 240
0
votes
0
replies
802
views
R package to calculate ancestral state characters using maximum parsimony?
R maximum parsimony ancestral states
3.7 years ago by DNAngel ▴ 240
0
votes
2
replies
5.0k
views
Is there a tool to calculate sequence similarity of sequences in a MSA?
alignment DNA
3.7 years ago by DNAngel ▴ 240
0
votes
0
replies
811
views
Theory question on dN/dS values for phylogeny
dNdS paml codeml
3.8 years ago by DNAngel ▴ 240
1
vote
7
replies
2.2k
views
Help with understanding PAML M0 output
PAML M0
updated 3.8 years ago by ★ 1.2k • written 3.8 years ago by ▴ 240
5
votes
4
replies
1.7k
views
Does Whole Exome Sequencing Include Mitochondrial Genome??
mitogenome exome whole exome sequencing
updated 3.8 years ago by 21k • written 3.8 years ago by ▴ 240
63 results • Page 1 of 2
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