User: wjidea

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wjidea40
Reputation:
40
Status:
New User
Location:
United States
Last seen:
3 days, 3 hours ago
Joined:
6 years, 2 months ago
Email:
w*****@gmail.com

about me

Posts by wjidea

<prev • 14 results • page 1 of 2 • next >
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Comment: C: Problem with fastq file
... seems like an unicode-encoding problem. what system are you using? ...
written 3 days ago by wjidea40
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Comment: C: Finding out if certain SNP positions fall into certain gene regions
... it seems like there was a discussion about this: https://www.biostars.org/p/95062/#95067 ...
written 10 weeks ago by wjidea40
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Comment: C: FASTA Headers Not Useful from Database Download
... Here is one biopython solution: from Bio import Entrez Entrez.email = 'your@email.com' # tell NCBI who you are fetch = Entrez.efetch(db="nucleotide", id="AB046939", rettype="gb", retmode="text") result = fetch.read().split('\n') for line in result: # to ge ...
written 23 months ago by wjidea40
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Answer: A: FASTA Headers Not Useful from Database Download
... It seems like the last part of the sequence header could lead you a taxid in NCBI GenBank. My solution: parse fasta -> last part of your header (VTX00166) -> search entrez (e.g., API in biopython) -> get taxon id -> translate taxon id using taxdump -> get taxonomy info -> modify ...
written 24 months ago by wjidea40
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Answer: A: Switching RepeatMasker off in Maker-P
... If you have the repeat mask features prepared in a GFF file, you can just load to MAKER-P in the maker opt control file and then turn off the repeat mask step in MAKER opt control file. rm_gff= #pre-identified repeat elements from an external GFF3 file ...
written 2.0 years ago by wjidea40
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Comment: C: degenerate nucleotide in abyss assemblies?
... What is the consequence to not have the PopBubbles step then? ...
written 2.0 years ago by wjidea40
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Comment: C: What Does The Zero Mapping Quality Mean For The Bwa Mapper?
... I agree, if the read mapped to a different chromosome, for example, the mapping quality could be 0 as well. ...
written 2.2 years ago by wjidea40
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Answer: A: Mummer alignment of two chromosomes
... I will answer to my own question then. I was trying to look for a flag I can modify to solve this problem. However, I didnt find a solution from Mummer itself. Therefore, I decided to use a stupid method combining blastn and python::faidx. I posted my solution to github gist, see below: \gist bc53e ...
written 3.0 years ago by wjidea40
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Mummer alignment of two chromosomes
... I was trying to align two full chromosome sequences (one contig for each chromosome) with Mummer v3.1, and I get mummer dot plot to visualize the alignment. These two chromosomes were actually very similar, however, the aligned region (red dots) were not shown on the diagonal. I am wondering is ther ...
mummer alignment written 3.0 years ago by wjidea40
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Comment: C: Model based structure analysis
... Could you please include some details about the programs or scripts you were using for generating those plots? Thx ...
written 3.3 years ago by wjidea40

Latest awards to wjidea

Popular Question 10 months ago, created a question with more than 1,000 views. For Mummer alignment of two chromosomes
Popular Question 5.4 years ago, created a question with more than 1,000 views. For Any Substitution For Genemapper?

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