Moderator: Haibao Tang

gravatar for Haibao Tang
Haibao Tang2.9k
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Location:
Richmond, CA
Website:
http://genomedata.tumb...
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tanghaibao
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Last seen:
4 months, 4 weeks ago
Joined:
7 years, 5 months ago
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Ph. D. in Plant Biology. I am interested in large scale data analysis and comparison of genome structures. I am also interested in the regulatory changes associated with the domestication process of cereal crops. Check out my github and blog.

Posts by Haibao Tang

<prev • 89 results • page 1 of 9 • next >
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Answer: A: De Novo Assembly And Comparative Genomics
... Align your Trinity transcripts, not individual reads, to the related genome is your best bet. It is unclear how close your species is to related references, but they might have good amounts of DNA substitutions in between. Therefore you need an alignment tool that is more sensitive. Popular choices ...
written 5.3 years ago by Haibao Tang2.9k
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Comment: C: Scan Through Txt, Append Certain Data To An Empty List In Python
... Hi, I am sure you will get an answer here, but you will benefit more by learning python a bit longer. A good place is (http://www.diveintopython.net/). This problem is a good practice for your python skills! ...
written 5.6 years ago by Haibao Tang2.9k
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Comment: C: Haldane Map Function And Genetic Linkage
... @unknown (google): it is not clear to me where your intuition comes from. 100Mb is a very large distance, it could be the two ends of a chromosome in human. I wouldn't expect strong linkage across that distance. Unless you really meant 100Kb rather than 100Mb - for example if snp A is 100Kb away fro ...
written 5.6 years ago by Haibao Tang2.9k
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Comment: C: Haldane Map Function And Genetic Linkage
... @unknown (google): see the plot above (x-axis is r, y-axis is m), remember 100cM = 1 morgan, and when you look at m = 1, r is somewhere between 0.4 and 0.5. Sean gave an exact calculation. ...
written 5.6 years ago by Haibao Tang2.9k
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Comment: C: Unexpected Small Genome Assembly
... @lh3: You are right about ALLPATHS-LG. It sounds like the OP has a range of insert sizes of PEs and mate pairs, but it is not clear if he has the "overlapping paired-end library" required by ALLPATHS. ...
written 5.6 years ago by Haibao Tang2.9k
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Answer: A: Unexpected Small Genome Assembly
... CLC de novo assembler is fast but not very accurate, its scaffolding ability is limited. The default contig size cutoff for CLC is 200. Based on my experience, I'd say your case falls within my expectation. For your data setup, I encourage you to try a different assembler - SOAPdenovo or ALLPATHS ( ...
written 5.6 years ago by Haibao Tang2.9k
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Answer: A: Haldane Map Function And Genetic Linkage
... You are right about using a map function. See a derivation here. The relationship between map unit and recombination frequency is: When r is small, r and m is roughly equal - so you are right about 1cM ~ 1% of the generation. It does not hold when r is approaching 0.5. ...
written 5.6 years ago by Haibao Tang2.9k
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Comment: C: Recommendations For Python Vcf Parser/Writer?
... thanks. any idea why UPPERCASE field names? ...
written 5.7 years ago by Haibao Tang2.9k
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Comment: C: Tools For Calculating Ld For Ngs Genomic Data And Generating Ld Decay Plot
... Since you expect LD to decay within the 25Kb window, you don't really need to calculate r2, say, two distant SNPs on two ends of the chromosome. How about splitting it up into small chunks? ...
written 5.7 years ago by Haibao Tang2.9k
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Answer: A: Gap Continuation Penalty With Dynamic Programming ?
... See the introductory slides here. I think you understand how to fill the DP matrix. For each cell in the DP matrix, we pick the max of three directions from three adjacent cells: UP, LEFT, DIAGONAL. UP and LEFT give you one gap, DIAGONAL give you match/mismatch. Now the affine gap penalty makes the ...
written 5.7 years ago by Haibao Tang2.9k

Latest awards to Haibao Tang

Popular Question 6 months ago, created a question with more than 1,000 views. For Multiple Sequence Alignment For Cdnas
Great Question 15 months ago, created a question with more than 5,000 views. For Multiple Sequence Alignment For Cdnas
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Where Can I Find The Old Tigr Ids?
Appreciated 15 months ago, created a post with more than 5 votes. For C: Scan Through Txt, Append Certain Data To An Empty List In Python
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Confuse About Sequence Assembly Results
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Ultra-Conservation In Genome Comparisons
Guru 3.5 years ago, received more than 100 upvotes.
Autobiographer 3.5 years ago, has more than 80 characters in the information field of the user's profile.
Supporter 3.5 years ago, voted at least 25 times.
Appreciated 5.6 years ago, created a post with more than 5 votes. For C: Scan Through Txt, Append Certain Data To An Empty List In Python
Commentator 5.6 years ago, created a comment with at least 3 up-votes. For C: Scan Through Txt, Append Certain Data To An Empty List In Python
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Haldane Map Function And Genetic Linkage
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Where Can I Find The Old Tigr Ids?
Good Answer 5.9 years ago, created an answer that was upvoted at least 5 times. For A: Where Can I Find The Old Tigr Ids?
Appreciated 5.9 years ago, created a post with more than 5 votes. For A: Where Can I Find The Old Tigr Ids?
Appreciated 5.9 years ago, created a post with more than 5 votes. For A: Getting The Error Probability Statistics From A (Large) Fastq File
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Getting The Error Probability Statistics From A (Large) Fastq File
Teacher 5.9 years ago, created an answer with at least 3 up-votes. For A: Bacterial Annotation Pipeline
Commentator 6.0 years ago, created a comment with at least 3 up-votes. For C: When Reviewing A Software Paper, Do You Talk About The Code Quality?
Good Answer 6.0 years ago, created an answer that was upvoted at least 5 times. For A: Is Is Feasible To Produce Intron Gff According To Utr Gff And Cds Gff?
Appreciated 6.0 years ago, created a post with more than 5 votes. For A: Is Is Feasible To Produce Intron Gff According To Utr Gff And Cds Gff?
Teacher 6.0 years ago, created an answer with at least 3 up-votes. For A: Is Is Feasible To Produce Intron Gff According To Utr Gff And Cds Gff?
Teacher 6.1 years ago, created an answer with at least 3 up-votes. For A: Confuse About Sequence Assembly Results
Teacher 6.1 years ago, created an answer with at least 3 up-votes. For A: Human Readable Multiple Sequence Alignment Format
Teacher 6.1 years ago, created an answer with at least 3 up-votes. For A: Read Location From Amos File

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