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0
votes
5
replies
672
views
Samtools unmapped reads
samtools
9 months ago by DNAngel ▴ 240
0
votes
3
replies
739
views
Samtools mapped and unmapped flags, what is the difference between the flags?
samtools
9 months ago by DNAngel ▴ 240
2
votes
2
replies
484
views
How do you get functional/biological role of motifs?
JASPAR
updated 10 months ago by 4.2k • written 10 months ago by ▴ 240
2
votes
8
replies
901
views
How to get names and class information from a list of target IDs from the JASPAR database?
JASPAR
updated 10 months ago by 78k • written 10 months ago by ▴ 240
3
votes
3
replies
570
views
Program to detect cis-regulatory modules for a non model species?
factors transcription
12 months ago by DNAngel ▴ 240
4
votes
3
replies
606
views
How do you find transcription factors in a newly sequenced genome?
interproscan factors transcription
updated 13 months ago by ▴ 20 • written 13 months ago by ▴ 240
7
votes
8
replies
756
views
How do you obtain a list of transcription factors from a genome?
transcription-factor
updated 8 months ago by 41k • written 13 months ago by ▴ 240
0
votes
6
replies
1.2k
views
Confused about which database to use - nt or nr?
blast
updated 14 months ago by 11k • written 14 months ago by ▴ 240
0
votes
2
replies
577
views
What happened to the SparCC github repository?
sparcc
updated 19 months ago by ★ 1.8k • written 19 months ago by ▴ 240
2
votes
8
replies
3.0k
views
Why does Kraken2 not produce taxon percentages with --report flag?
kraken2
updated 23 months ago by ▴ 90 • written 2.6 years ago by ▴ 240
0
votes
0
replies
534
views
Can I use DESeq2 to analyze my abundance dataset, which also happens to have a lot of zeros?
deseq2
2.1 years ago by DNAngel ▴ 240
2
votes
4
replies
1.2k
views
WGCNA, what does it mean if no hub genes are identified?
WGCNA
2.2 years ago by DNAngel ▴ 240
1
vote
0
replies
524
views
R package for determining best model transformation for a dataset?
R
2.2 years ago by DNAngel ▴ 240
11
votes
15
replies
2.8k
views
Output of samtools view, what does the third column actually represent?
samtools
updated 2.2 years ago by 18k • written 2.2 years ago by ▴ 240
0
votes
0
replies
489
views
How to find out how many reads were used in contig assembly in metaSPADES?
metaspades
2.2 years ago by DNAngel ▴ 240
1
vote
1
reply
1.2k
views
How do you interpret Tukey's significance when there is no group clustering alone?
Tukey
2.2 years ago by DNAngel ▴ 240
1
vote
1
reply
1.1k
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 2.3 years ago by 136k • written 2.3 years ago by ▴ 240
0
votes
0
replies
447
views
R vegdist does not compute distances for all my sites
vegan vegdist R
updated 2.3 years ago by 41k • written 2.3 years ago by ▴ 240
3
votes
1
reply
1.6k
views
What is the recommended contig length to filter?
metaspades
updated 2.4 years ago by ★ 25k • written 2.4 years ago by ▴ 240
2
votes
6
replies
960
views
Is there a different names.dmp file in the taxonomy name/id browser?
ncbi
updated 2.4 years ago by 136k • written 2.4 years ago by ▴ 240
1
vote
11
replies
1.5k
views
Blast 2.11 not blasting all sequences in a file?
blast
2.4 years ago by DNAngel ▴ 240
7
votes
12
replies
1.4k
views
7 follow
Why do I lose sequences when converting my bam files into fastq?
fastq bam bamToFastq
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 240
0
votes
0
replies
599
views
Confused about sambamba syntax for unmapped and mapped
sambamba
2.5 years ago by DNAngel ▴ 240
2
votes
2
replies
606
views
Does spades/metaspades normally having missing nodes?
metaspades spades
2.5 years ago by DNAngel ▴ 240
3
votes
5
replies
1.1k
views
How to use lapply to extract taxonomic information in my species list?
R
2.5 years ago by DNAngel ▴ 240
0
votes
2
replies
518
views
How to get domain/kingdom name in a table of taxid in R tidyverse?
R
2.5 years ago by DNAngel ▴ 240
2
votes
3
replies
2.8k
views
kraken2 unclassified output does not work with paired reads?
Kraken2
updated 2.5 years ago by 99k • written 2.5 years ago by ▴ 240
1
vote
1
reply
1.2k
views
Best method to visualize metagenomic data besides krona?
metagenomics krona
updated 2.5 years ago by 3.5k • written 2.5 years ago by ▴ 240
3
votes
6
replies
2.4k
views
Bamtools stats and samtools flagstat produce different results and confusing my sambamba output.
sambamba bamtools samtools
2.5 years ago by DNAngel ▴ 240
0
votes
6
replies
2.2k
views
What do you do with the data processed after running metaspades/spades?
metaspades spades
updated 2.6 years ago by 3.5k • written 2.6 years ago by ▴ 240
0
votes
2
replies
727
views
What to do with mapped reads after assembly?
Assembly annotation
2.8 years ago by DNAngel ▴ 240
0
votes
11
replies
1.2k
views
Error when trying to convert BAM file to FASTQ.
samtools bedtools
2.8 years ago by DNAngel ▴ 240
0
votes
6
replies
1.5k
views
FastQC Per sequence GC count always fails after trimmomatic?
fastqc trimmomatic
updated 2.8 years ago by 136k • written 2.8 years ago by ▴ 240
2
votes
13
replies
6.2k
views
How do you download the nt database for Kraken2?
Kraken2 nt
updated 2.8 years ago by 136k • written 2.8 years ago by ▴ 240
0
votes
6
replies
787
views
Papers/posts on best practises for dealing with Illumina reads?
assembly trimmomatic bwa-mem
updated 2.8 years ago by 78k • written 2.8 years ago by ▴ 240
0
votes
2
replies
519
views
Determining if the number of significant results between two categories is significantly different?
statistics
3.1 years ago by DNAngel ▴ 240
0
votes
0
replies
436
views
How to know if it is missing a gene or assembly error?
BWA Assembly
updated 6 months ago by 41k • written 3.1 years ago by ▴ 240
0
votes
0
replies
489
views
PAML sample size question and variation in results
PAML
3.1 years ago by DNAngel ▴ 240
0
votes
0
replies
914
views
Understanding PAML results between random-sites and clade model C.
PAML
3.2 years ago by DNAngel ▴ 240
2
votes
3
replies
1.6k
views
How to parallelize bwa mem for single-end data within a larger bash script?
bash bwa-mem gnu-parallel
updated 4.1 years ago by 158k • written 4.1 years ago by ▴ 240
2
votes
2
replies
1.9k
views
How do you extract longest transcript from fasta file using length and header IDs?
awk fasta
updated 4.1 years ago by 13k • written 4.1 years ago by ▴ 240
2
votes
1
reply
1.7k
views
How to loop over a directory to set each file as a variable?
bash
4.1 years ago by DNAngel ▴ 240
3
votes
7
replies
1.3k
views
Does Abyss work on single-end Illumina reads only?
Abyss
updated 4.1 years ago by 8.2k • written 4.1 years ago by ▴ 240
4
votes
6
replies
1.9k
views
How do you assemble contigs without using a reference genome?
assembly genome
updated 4.2 years ago by 35k • written 4.2 years ago by ▴ 240
1
vote
6
replies
1.9k
views
What do you do after obtaining sorted bam files?
bwa bam
updated 4.2 years ago by 13k • written 4.2 years ago by ▴ 240
0
votes
0
replies
709
views
How to obtain protein-coding sequences from assembled genome/exome dataset?
PAML bwa
4.2 years ago by DNAngel ▴ 240
0
votes
0
replies
634
views
How to test evolutionary rates for each species in a gene alignment?
evolutionary rate R
4.3 years ago by DNAngel ▴ 240
0
votes
0
replies
924
views
R package to calculate ancestral state characters using maximum parsimony?
R maximum parsimony ancestral states
4.5 years ago by DNAngel ▴ 240
0
votes
2
replies
5.8k
views
Is there a tool to calculate sequence similarity of sequences in a MSA?
alignment DNA
4.5 years ago by DNAngel ▴ 240
0
votes
0
replies
915
views
Theory question on dN/dS values for phylogeny
dNdS paml codeml
4.6 years ago by DNAngel ▴ 240
65 results • Page 1 of 2
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