User: LRStar

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LRStar190
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190
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United States
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6 years, 2 months ago
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Posts by LRStar

<prev • 66 results • page 1 of 7 • next >
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Comment: C: Determine NCBI Nucleotide source of .fasta amino acid file
... Thanks @gb. I believe it is the first one. What was your process for determining that? I have a few other files like this and believe perhaps my navigation skill son NCBI Nucleotide are not up to par... because I often cannot reverse engineer and figure out where my files came from. (Yes, I plan to ...
written 5 days ago by LRStar190
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Determine NCBI Nucleotide source of .fasta amino acid file
... I have a .fasta file with amino acid sequences. The beginning of the file is as follows: >lcl|NC_019674.1_prot_1 [locus_tag=BN341_RS00005] [protein=OmpA family protein] [pseudo=true] [location=join(1804546..1804601,1..456)] [gbkey=CDS] MKKWFLAAAVVACVLMTGCPPRLKKPPPPPNPPPNLKNTPCPKKRPRPSP*K ...
fasta ncbi nucleotide written 5 days ago by LRStar190 • updated 18 hours ago by genomax76k
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General pipeline for determining which tissues plasma cfDNA came from
... In human plasma samples, there are circulating RNA, DNA, and microRNA. This is an improvement over the alternative method of taking solid tissue biopsies. However, I imagine that scientists would like to infer which tissues each of these circulating molecules originated from. 1) Is there an establi ...
cfdna liquidbiopsy written 12 days ago by LRStar190
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... @genomax Thank you for your comments. I used BWA to align each sample to the reference genome (H. cetorum MIT 00-7128). Then, I used Qualimap to assess the alignment. The first sample had 85% mapping rate, but the other samples (which all seem similar to each other and are the ones I am struggling w ...
written 3 months ago by LRStar190
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... @ctseto. I am attempting to map the reads to a host genome (and also run QUAST on my metaspades contigs using the host genome as a reference). This might be a very basic question, but I am unsure how to download an appropriate (at least starting point) reference genome for dolphin. 1) I tried typin ...
written 3 months ago by LRStar190
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... So cool. I have never done that procedure before and will likely start doing so especially with these datasets that seem like they need thorough cleaning. ...
written 3 months ago by LRStar190
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... Thanks @ctseto. I am embarrassed to say I am not entirely sure whether I am using Kraken1 or Kraken2. I have been using Kraken on Galaxy Version 1.2.4. I was unable to install Kraken locally but will very likely try again. ...
written 3 months ago by LRStar190
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... Thank you @ctseto. I was unaware of the Baylor HGSC dolphin genome project and can look into using it as a host genome. I am sorry to ask, but could you kindly expand on "f13 + f64/f128 for read one and read two"? I tried Googling those values but remain a bit clueless. Thank you very much again for ...
written 3 months ago by LRStar190
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... @ctseto Thank you for your comment. It might take me a while to get to performing a binning job (using VizBin I think with what you suggested earlier), but I look forward to trying it too. Conceptually, if I see redundancy and there are assembly artifacts, as you state, would there be a program to r ...
written 3 months ago by LRStar190
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Comment: C: How to determine species of paired-end .fastq files (low mapping rates and incon
... Thank you so much @genomax. I agree with your sentiment about letting the data speak for itself. My advisor is wetlab by background and does not work with command-line tools. He just noticed on CLC Genomics Workbench that less stringent parameters made the data map better to Helicobacter. His thinki ...
written 3 months ago by LRStar190

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Terminology question: Phylogenetic tree duplicated generation counts
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Great Question 17 months ago, created a question with more than 5,000 views. For Preparing a .genome file for snpEff
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Epic Question 23 months ago, created a question with more than 10,000 views. For Convert .Gff3 File To 12-Column .Bed File
Popular Question 23 months ago, created a question with more than 1,000 views. For Terminology question: Phylogenetic tree duplicated generation counts
Great Question 3.7 years ago, created a question with more than 5,000 views. For Convert .Gff3 File To 12-Column .Bed File
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