User: Dave Carlson
Dave Carlson • 510
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- Stony Brook University, NY
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- 1 day, 6 hours ago
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- 5 years, 1 month ago
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Posts by Dave Carlson
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... Diamond only works for protein alignment (i.e., blastp or blastx). This is a nucleotide alignment question. ...
written 3 days ago by
Dave Carlson • 510
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... Are you limiting your blast search to a single HSP with `-max_hsps 1`? If not, that may be what's causing you to get multiple results from the same sequence. Depending on what your ultimate goal for the analysis is, you may actually want to keep multiple HSPs per matching sequence. ...
written 10 days ago by
Dave Carlson • 510
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... It looks like you're using the repeats from the Dfam database. Is your genome from a species that is present in Dfam (or closely related to one)? If not, perhaps the evolutionary distance between your species and the species in Dfam is making it hard to accurately identify your TEs?
When I run Repe ...
written 12 days ago by
Dave Carlson • 510
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... Results for assembling a highly repetitive 1 Gb plant genome with ~100x coverage PE Illumina data: 300 Mb assembly (1/3 of the genome)
Results for assembling the same genome with ~100x Sequel 1 PacBio reads: 950 Mb genome (~90% of the genome)
These days, I wouldn't even attempt genome assembly wit ...
written 13 days ago by
Dave Carlson • 510
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... In addition to the previously mentioned PlantC-values Database, there is the [Animal Genome Size Database][1]
[1]: http://www.genomesize.com/ ...
written 19 days ago by
Dave Carlson • 510
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... [Here's][1] python 3 solution using Biopython with regular expressions:
#!/usr/bin/env python
import argparse
import re
import sys
from Bio import SeqIO
parser = argparse.ArgumentParser(description="Search for pattern in fasta header and return sequences whose head ...
written 21 days ago by
Dave Carlson • 510
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Comment:
C: bcftools variant calling
... I don't know of a better paper, I'm afraid. I believe that Li 2011 describes the algorithms used by samtools/bcftools for calculating genotype likelihoods and calling variants. There is also a --multiallelic calling model implemented in more recent versions of bcftools, which is briefly described [ ...
written 22 days ago by
Dave Carlson • 510
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Answer:
A: bcftools variant calling
... You probably want to check out [Li 2011][1]:
**A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data**
Abstract
>Motivation: Most existing methods for DNA sequence analysis
> rely on accurate seque ...
written 24 days ago by
Dave Carlson • 510
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... Hi Russel,
I believe something like the following will work for your cutadapt command:
parallel --verbose --link 'cutadapt -a AGATCGGAAGAG -A AGATCGGAAGAG -o {1.}.trimmed.fastq -p {2.}.trimmed.fastq {1} {2} > {1.}_cutadapt.txt' ::: *R1_001.fastq ::: *R2_001.fastq
In the case of the filenam ...
written 9 weeks ago by
Dave Carlson • 510
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... I realize that this is not a direct answer to your question, but you should not expect to have any reliable stats from DESeq if you don't have biological replicates. This has been discussed extensively. See for example:
https://www.biostars.org/p/398152/
Also the [latest DESeq2 vignette][1] gives ...
written 11 weeks ago by
Dave Carlson • 510
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For A: Assembler for only nanopore data
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For A: Up-to-date Online RNA Sequence Analysis Training/Courses/Papers?
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For A: Genome duplication assessment
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For codeml jobs taking much longer on a server than on an imac
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