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Moderator: Damian Kao

gravatar for Damian Kao
Damian Kao ♦ 15k
Reputation:
15,190
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Location:
USA
Website:
http://blog.nextgeneti...
Last seen:
1 day, 2 hours ago
Joined:
7 years, 7 months ago
Email:
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Bioinformatician at Janelia Research Campus.

Posts by Damian Kao

<prev • 911 results • page 1 of 92 • next >
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Comment: C: Is there a preferred RNA-seq aligner for (very) short reads and potential homolo
... Try setting --outFilterMatchNmin to 20 to see if you can get more mapping. However, that means it only requires 20 bases to map, which is pretty low. ...
written 4 weeks ago by Damian Kao ♦ 15k
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Answer: A: Does Gene length corrected TMM [GeTMM] violate any assumptions of TMM normalizat
... Technically, RPK values do not violate assumptions of TMM. TMM is just a technique that tries to find the non-DE portion of the expression distribution by very liberally trimming off outliers. It doesn't matter what kind of expression units you are using. However, RPK values do violate assumptio ...
written 4 weeks ago by Damian Kao ♦ 15k
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Answer: A: Trimmomatic output file Issue
... It looks like you are not specifying an output file for the -trimlog parameter. So it thinks your `output_forward_paired.fq.gz` is an input. I hope you still can still redownload `sample1_R1_001.fastq.gz`, because it might have been overwritten. ...
written 4 weeks ago by Damian Kao ♦ 15k
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Answer: A: Code golf: detecting homopolymers of length N in the (human) genome
... Takes in fasta file and a second parameter for homopolymer length. It streams through each line to find homopolymers. Outputs chromosome, start, end, homopolymer base, length of homopolymer. I tested it out on this fasta file: >A AGTCAAAA GGGGTTTTCCCC >B AGTCCCCCTTTTAAA ...
written 5 weeks ago by Damian Kao ♦ 15k
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Answer: C: Getting the number of SNPs in some ranges
... You have a .csv file with chromosome, start, end coordinates. You can change that into a .bed file pretty easily. Same with your SNP csv file. Convert those csv files to bed and then use bedtools intersect. ...
written 8 weeks ago by Damian Kao ♦ 15k
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Comment: C: Strange Depth of Coverage distribution
... Yeah that could be it. You can check this by looking at the insert size distribution of your PE reads. See if it is smaller than 2 * average read length. The 9th column of your .sam/.bam should be the insert size. ...
written 11 weeks ago by Damian Kao ♦ 15k
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Comment: C: Getting read depth for normal and tumour
... I am not sure what program you are using to generate the .vcfs. But you should look into the manual of the program and see if it outputs depths using the format fields in the vcf. For example, you have "DP" field in your vcf that shows the depth of the individual samples. Perhaps one of the other f ...
written 11 weeks ago by Damian Kao ♦ 15k
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Comment: C: Getting read depth for normal and tumour
... Can you post a couple of lines of your vcf file? ...
written 11 weeks ago by Damian Kao ♦ 15k
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Answer: A: Samtools segmentation fault when extracting exons from bam file.
... There is a -L flag that you can use with samtools to output alignments overlapping intervals defined by a .bed file. That's probably your best option. You'll have to convert your exons.txt to a bed file. ...
written 11 weeks ago by Damian Kao ♦ 15k
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Comment: C: Strange Depth of Coverage distribution
... Even if multiple samples were mixed together in the depth of cov reporting, it should not show this distribution. Multi-sample mix should show a smooth histogram with potentially multiple peaks. Maybe try using samtools stats' depth of coverage info for plotting and see if you get the same thing. Pe ...
written 12 weeks ago by Damian Kao ♦ 15k

Latest awards to Damian Kao

Appreciated 23 days ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 28 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
Scholar 28 days ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Scholar 4 weeks ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 8 weeks 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 11 weeks ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 11 weeks 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
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: A Farewell To Bioinformatics
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Popular Question 5 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Teacher 6 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 7 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Scholar 10 months ago, created an answer that has been accepted. For C: Does trinity discard reads shorter than 25-mer?
Scholar 10 months ago, created an answer that has been accepted. For C: What's the correct way to withdraw a published database/server ?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: A Farewell To Bioinformatics
Appreciated 10 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 10 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 10 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 10 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 11 months ago, created a question with more than 1,000 views. For deseq2 user defined size factors
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Shall We Go Back To Stackexchange?
Appreciated 13 months ago, created a post with more than 5 votes. For A: A Farewell To Bioinformatics
Teacher 14 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
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