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8
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12
replies
6.4k
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What is the most optimal way to count the nucleotide bases of each fastq file in my directory using UNIX commands?
UNIX fastq bash
updated 3.7 years ago by 36k • written 9.4 years ago by ▴ 20
0
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851
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Comment: C: Best way to download a subsection of a genome that matches a search query on NCB
4.3 years ago by Tom ▴ 20
0
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3
replies
851
views
Best way to download a subsection of a genome that matches a search query on NCBI's Blast?
blast ncbi alignment
4.3 years ago by Tom ▴ 20
2
votes
11
replies
2.7k
views
How would I use BioPython to mass download some assemblies from NCBI?
ncbi biopython
updated 4.7 years ago by 152k • written 4.7 years ago by ▴ 20
0
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2
replies
2.5k
views
How do I suppress warnings on command line blast?
blast command line
5.4 years ago by Tom ▴ 20
0
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1
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2.9k
views
Comment: C: Where in the source code for SeqIO.write() does the function write the IDs and a
updated 5.5 years ago by 45k • written 9.4 years ago by ▴ 20
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0
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2.9k
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Comment: C: Where in the source code for SeqIO.write() does the function write the IDs and a
updated 5.5 years ago by 45k • written 9.4 years ago by ▴ 20
0
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0
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22k
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Comment: C: Jellyfish-Kmer, Genome Size Estimation
updated 5.5 years ago by 45k • written 9.5 years ago by ▴ 20
0
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1
reply
22k
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Comment: C: Jellyfish-Kmer, Genome Size Estimation
updated 5.5 years ago by 45k • written 9.5 years ago by ▴ 20
0
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1
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5.4k
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Comment: C: How would you write script to count all kmers to estimate the genome size, simil
updated 5.5 years ago by 45k • written 9.5 years ago by ▴ 20
0
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1
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5.4k
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Comment: C: How would you write script to count all kmers to estimate the genome size, simil
updated 5.5 years ago by 45k • written 9.6 years ago by ▴ 20
0
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1
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2.8k
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Comment: C: Where does Kmergenie get it's y axis numbers from? Is it suppose to be the local
updated 5.5 years ago by 45k • written 9.6 years ago by ▴ 20
4
votes
6
replies
4.0k
views
In Jellyfish, what does the "-C" switch do?
Jellyfish Kmer Assembly
updated 8.5 years ago by 20 • written 9.6 years ago by ▴ 20
0
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1
reply
3.8k
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Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
9.0 years ago by Tom ▴ 20
0
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0
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3.8k
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Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
9.0 years ago by Tom ▴ 20
0
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0
replies
3.8k
views
Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
9.0 years ago by Tom ▴ 20
0
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0
replies
3.8k
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Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
9.0 years ago by Tom ▴ 20
0
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0
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3.8k
views
Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
9.0 years ago by Tom ▴ 20
0
votes
2
replies
3.8k
views
Comment: C: How do I count the number of nucleotides using jellyfish; can I obtain the numbe
9.0 years ago by Tom ▴ 20
4
votes
13
replies
3.8k
views
How do I count the number of nucleotides using jellyfish; can I obtain the number of nucleotides that went into a mer_counts.jf from jellyfish stats?
jellyfish genomics k-mer kmer
9.0 years ago by Tom ▴ 20
0
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1
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2.8k
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Comment: C: What are some drawbacks in using highly conserved genes to determine genomic com
9.1 years ago by Tom ▴ 20
0
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1
reply
2.8k
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Comment: C: What are some drawbacks in using highly conserved genes to determine genomic com
9.1 years ago by Tom ▴ 20
0
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0
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2.8k
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Comment: C: What are some drawbacks in using highly conserved genes to determine genomic com
9.1 years ago by Tom ▴ 20
0
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10
replies
2.8k
views
What are some drawbacks in using highly conserved genes to determine genomic completeness?
genome bacteria sequencing Assembly
updated 9.1 years ago by ★ 1.2k • written 9.1 years ago by ▴ 20
2
votes
2
replies
2.2k
views
I have a genbank file and a list of addresses. I'd like to pull the exact nucleotide that corresponds to that address in biopython. How would I do t…
CLCBio BioPython
updated 9.2 years ago by 6.0k • written 9.2 years ago by ▴ 20
2
votes
5
replies
2.6k
views
Is there a specific option in BioPython that lets you call the gene name given an address of a nucleotide?
BioPython
updated 9.2 years ago by ★ 1.8k • written 9.2 years ago by ▴ 20
0
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1
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2.6k
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Comment: C: Is there a specific option in BioPython that lets you call the gene name given a
9.2 years ago by Tom ▴ 20
0
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3
replies
2.5k
views
How would you create a table for multiple organisms vs presence of multiple genes using command line blast? [image in description]
blast command line blastp
updated 9.3 years ago by 55k • written 9.3 years ago by ▴ 20
0
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0
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2.5k
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Comment: C: How would you create a table for multiple organisms vs presence of multiple gene
9.3 years ago by Tom ▴ 20
0
votes
1
reply
2.5k
views
How do I get SeqIO.write() to make a genbank file that includes the REFERENCE field?
genbank python SeqIO biopython
updated 2.9 years ago by 45k • written 9.4 years ago by ▴ 20
0
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1
reply
2.9k
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Comment: C: Where in the source code for SeqIO.write() does the function write the IDs and a
9.4 years ago by Tom ▴ 20
0
votes
6
replies
2.9k
views
Where in the source code for SeqIO.write() does the function write the IDs and annotations to a new genbank file?
python seqio biopython
updated 2.9 years ago by 45k • written 9.4 years ago by ▴ 20
3
votes
2
replies
2.8k
views
Is there a concensus on which k-mers should be counted in a histogram graph of kmer multiplicity vs frequency to estimate the genome size?
kmergenie kmer jellyfish genome
updated 2.9 years ago by 45k • written 9.5 years ago by ▴ 20
0
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0
replies
5.4k
views
Comment: C: How would you write script to count all kmers to estimate the genome size, simil
9.5 years ago by Tom ▴ 20
0
votes
1
reply
22k
views
Comment: C: Jellyfish-Kmer, Genome Size Estimation
9.5 years ago by Tom ▴ 20
0
votes
1
reply
5.4k
views
Comment: C: How would you write script to count all kmers to estimate the genome size, simil
9.5 years ago by Tom ▴ 20
0
votes
9
replies
5.4k
views
How would you write script to count all kmers to estimate the genome size, similar to the one in kmergenie, by using jellyfish+python instead? How wo…
Jellyfish R Python kmer Kmergenie
updated 2.9 years ago by 45k • written 9.6 years ago by ▴ 20
0
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0
replies
2.3k
views
Comment: C: [Experimental Design] Is it possible to determine completeness of a genome if yo
9.6 years ago by Tom ▴ 20
3
votes
2
replies
2.3k
views
[Experimental Design] Is it possible to determine completeness of a genome if you were given raw reads?
sequencing genome theory coverage
updated 9.6 years ago by 6.2k • written 9.6 years ago by ▴ 20
0
votes
1
reply
4.0k
views
Comment: C: In Jellyfish, what does the "-C" switch do?
9.6 years ago by Tom ▴ 20
0
votes
1
reply
2.8k
views
Comment: C: Where does Kmergenie get it's y axis numbers from? Is it suppose to be the local
9.6 years ago by Tom ▴ 20
2
votes
8
replies
2.8k
views
Where does Kmergenie get it's y axis numbers from? Is it suppose to be the local maxima of each plot?
kmergenie kmer
updated 2.9 years ago by 45k • written 9.6 years ago by ▴ 20
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