Moderator: Damian Kao

gravatar for Damian Kao
Damian Kao15k
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Website:
http://blog.nextgeneti...
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7 years ago
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Bioinformatician at Janelia Research Campus.

Posts by Damian Kao

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Answer: A: Pulling out interval adjoining regions
... As with most interval operations, bedtools has a command for it: https://bedtools.readthedocs.io/en/latest/content/tools/flank.html ...
written 16 days ago by Damian Kao15k
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Comment: C: SNP calling from BAM file
... Can you please post the command you used and the error message. ...
written 28 days ago by Damian Kao15k
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Answer: C: RNA-seq normalization and standardization
... Packages like edgeR and DESeq2 don't actually transform the counts for DE analysis. A normalization factor is calculated and then used in the DE test. There are good information in the absolute counts for each gene. Standardization is not used, otherwise that information would be lost. ...
written 6 weeks ago by Damian Kao15k
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Comment: C: Abyss run time
... What's the estimated genome size of your organism? And how many reads do you have? ...
written 6 weeks ago by Damian Kao15k
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Comment: C: SNPGenie: CDS does not have length that is divisible by 3
... I think the problem you have with SNPGenie might not be related to CDS length not being a multiple of 3. What is the exact error message you get from SNPGenie? In the SNPGenie usage instructions: https://github.com/chasewnelson/SNPGenie It says that it reads the gene_id field to concatenate CDS li ...
written 6 weeks ago by Damian Kao15k
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Comment: C: SNPGenie: CDS does not have length that is divisible by 3
... Yes, it is true that CDS features in a gtf/gff file are broken up into multiple intervals when the gene is multi-exonic. Gene/Transcript features describe the entire gene from start of 5\` UTR to end of 3\` UTR. Exon features describe multiple exon intervals, including 5\`/3\` UTRs. CDS describes ...
written 7 weeks ago by Damian Kao15k
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Comment: C: SNPGenie: CDS does not have length that is divisible by 3
... There are potentially multiple CDS lines for each transcript in a .gtf file. Each CDS line define an interval that correspond to multiple exons. The length of each CDS line does not have to be in a multiple of three. But the sum length of multiple CDS lines for each transcript should be in a multipl ...
written 7 weeks ago by Damian Kao15k
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Comment: C: What are the recommended methods for merging de-novo assemblies?
... So you have 88 sets of metagenomic reads? I don't see why not just merge them all and treat them as one huge metagenomic read set and assemble that with metagenome aware assembler (metaSpades or something). And from the resulting assembly, pull out the contigs you want based on reference mapping. ...
written 7 weeks ago by Damian Kao15k
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Comment: C: Trinity ERROR during assembling extracted reads
... I would suggest using a newer version of Trinity. You are using a 2011 version. There has been a lot of new development since then that might fix your issue. ...
written 7 weeks ago by Damian Kao15k
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Answer: A: Where to find a valid GTF file for stringtie asssembly?
... The .gff file you downloaded doesn't describe gene annotations. It just describes the genome scaffolds/contigs. There doesn't appear to be any gene annotations in the NCBI ftp you posted. You do not need to provide StringTie with a set of reference annotations. You can perform an assembly just wit ...
written 7 weeks ago by Damian Kao15k

Latest awards to Damian Kao

Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Popular Question 5 weeks ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Scholar 4 months ago, created an answer that has been accepted. For C: Does trinity discard reads shorter than 25-mer?
Scholar 4 months ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: A Farewell To Bioinformatics
Appreciated 4 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Appreciated 4 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Popular Question 5 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Appreciated 7 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Removing Redundant Amino Acid Sequences From Fasta - *But Also Give The Groups O
Scholar 8 months ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Bwa What Is In .Sai File
Appreciated 8 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Good Question 9 months ago, asked a question that was upvoted at least 5 times. For Given Unlimited Resources, What Would Be Your Dream Experiment?
Appreciated 9 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Popular Question 9 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Popular Question 10 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: A Farewell To Bioinformatics
Popular Question 10 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Popular Question 11 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Appreciated 11 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics

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