User: John Smith

gravatar for John Smith
John Smith260
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260
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Location:
United States
Last seen:
2 years, 11 months ago
Joined:
5 years, 4 months ago
Email:
c********@yahoo.com

Posts by John Smith

<prev • 22 results • page 1 of 3 • next >
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Comment: C: Can one get the entire genome by putting all contigs together in this particular
... I am aligning the reads with Bowtie 2. Would I need to specify a certain parameter for Bowtie 2 since the FASTA file will contain several sequences (contigs in this case)? Or will it automatically recognize that there are several sequences in the FASTA file and attempt to align the reads? ...
written 5.3 years ago by John Smith260
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Comment: C: Can one get the entire genome by putting all contigs together in this particular
... I am trying to align raw sequencer data to the genome of BR1064. But it appears that there is no reference genome so I thought that maybe it was possible to just obtain it by putting all the contigs together. ...
written 5.3 years ago by John Smith260
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Can one get the entire genome by putting all contigs together in this particular case?
... I am still new to bioinformatics and I have not yet fully understood the definition of contig. I have read a few explanations and what I understand is that contigs are fragments of the genome for which we are certain that the order of the bases is correct. Then, we make scaffolds out of the contigs ...
genome sequence contig written 5.3 years ago by John Smith260 • updated 5.3 years ago by Philipp Bayer6.5k
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Comment: C: How to determine to which strains of S. pneumoniae these FASTQ files belong to?
... I solved it. One has to delete the cookies for the site and then open it again. Apparently there is a buggy script running on the site. ...
written 5.3 years ago by John Smith260
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Comment: C: How to determine to which strains of S. pneumoniae these FASTQ files belong to?
... I see, I tried the link before and I just assumed that the site was broken since it did not work for Firefox in my version of Ubuntu nor for Chromium. It worked on Firefox on Windows but I had to ask a script on the site to stop running before I could navigate. I thought I was missing something obvi ...
written 5.3 years ago by John Smith260
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How to determine to which strains of S. pneumoniae these FASTQ files belong to?
... This is a continuation to my previous question. I am working with this study given in the answer to the question. I realized that I can look up the reference genome of many strains in the "Assembly" section of the ENA search results but I cannot figure out to which specific strains of S. pneumoniae ...
pneumoniae strains fastq written 5.3 years ago by John Smith260 • updated 5.3 years ago by Devon Ryan92k
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Comment: C: Where can I find the raw sequencer output of two strains of S. pneumoniae (FASTQ
... I am having trouble understanding the different categories on the left of the search results (I am still new to bioinformatics). Should I look for the reference genome within "Assembly"? And should I look for the raw sequencer output within "Read" or within "Study"? Moreover, what is the difference ...
written 5.3 years ago by John Smith260
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Where can I find the raw sequencer output of two strains of S. pneumoniae (FASTQ format) along with their corresponding reference genomes (FASTA format)?
... I am looking for any two strains of S. pneumoniae for which I can find their raw output sequencer data in FASTQ format and for which I can find their reference genomes (since I plan to align the raw data in the FASTQ format to the reference genomes using Bowtie 2). I know that I could make artificia ...
fasta genome fastq rna-seq sequencing written 5.3 years ago by John Smith260 • updated 5.3 years ago by Dan D6.8k
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Comment: C: How to make Bowtie 2 align the following reads as pairs?
... I will try that. My background is not in biology so it was not clear to me what this section of the manual meant (despite understanding upstream/downstream and reverse complement). ...
written 5.3 years ago by John Smith260
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How to make Bowtie 2 align the following reads as pairs?
... This is somewhat of a continuation to my previous question here. Apparently, the problem with the paired-end artificial reads is that they have the following orientation: -----> read 1           -----> read 2 --------------------------------- DNA fragment Is there a Bowtie 2 configuration t ...
bowtie 2 paired end written 5.3 years ago by John Smith260 • updated 5.3 years ago by K.Nijbroek100

Latest awards to John Smith

Great Question 3.7 years ago, created a question with more than 5,000 views. For What read lengths are produced by modern Illumina sequencers?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For How do experienced people look for full reference genomes?
Popular Question 3.7 years ago, created a question with more than 1,000 views. For Why is the output of Artificial FASTQ Generator not aligning properly with Bowtie 2?
Popular Question 5.2 years ago, created a question with more than 1,000 views. For How do experienced people look for full reference genomes?
Popular Question 5.2 years ago, created a question with more than 1,000 views. For What read lengths are produced by modern Illumina sequencers?
Popular Question 5.2 years ago, created a question with more than 1,000 views. For Orientation in paired-end sequencing?
Supporter 5.3 years ago, voted at least 25 times.
Student 5.3 years ago, asked a question with at least 3 up-votes. For How do experienced people look for full reference genomes?
Good Question 5.3 years ago, asked a question that was upvoted at least 5 times. For How do experienced people look for full reference genomes?
Appreciated 5.3 years ago, created a post with more than 5 votes. For How do experienced people look for full reference genomes?
Student 5.3 years ago, asked a question with at least 3 up-votes. For How do experienced people look for full reference genomes?

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