User: Gww

gravatar for Gww
Gww2.6k
Reputation:
2,570
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Location:
Canada
Last seen:
3 months, 2 weeks ago
Joined:
7 years, 1 month ago
Email:
g********@gmail.com

PhD student working with bioinformatics and molecular biology.

Posts by Gww

<prev • 125 results • page 1 of 13 • next >
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Comment: C: Determine if two RNA-seq samples are repeats of each other
... You could do principle component analysis or look at the correlations between samples. Make sure to use between-sample normalized expression values. ...
written 16 months ago by Gww2.6k
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Comment: C: DESeq2 design matrix controlling for donor batches
... I will try that thank you. I am still having trouble understanding how these GLM based methods work. ...
written 17 months ago by Gww2.6k
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DESeq2 design matrix controlling for donor batches
... I have RNA-seq data from four different cell fractions derived from two different developmental stages. There are 5 replicates for one stage and 6 replicates for the other. I am currently attempting to mitigate an obvious batch effect due to the donor rather than the cell fraction (See the list of ...
R deseq2 rna-seq written 17 months ago by Gww2.6k
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Comment: C: Can Tophat Deal With Overlapping Transcripts When Given --Gtf ?
... That is not entirely true. Tophat may mispredict novel splice junctions by choosing a splicing motif from the wrong strand. ...
written 3.9 years ago by Gww2.6k
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Comment: C: Statistics: Tandem Repeat Enrichment Between Two Sets Of Sequences
... What paper is that figure from? ...
written 4.3 years ago by Gww2.6k
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Answer: A: Scary Exon Sizes
... I don't see any problems with your exon sizes or transcript sizes. If your transcript has one or more large introns its size could be quit large. Small exons (also known as microexons) are known to exist, for example, see Carlo et al (2000). ...
written 5.6 years ago by Gww2.6k
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Answer: A: Java Library For Reading Bai Files And Understanding Index With Respect To Bam
... The picard library implements samtools in java. For more specific information about how BAM files are indexed check out the samtools format specification. ...
written 5.7 years ago by Gww2.6k
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Answer: A: Weird Fastq Sequences
... Those read sequences are in colorspace rather than basespace, which means that the sequencing was performed using applied biosystems SOLiD sequencing technology. There are aligners that are capable of aligning reads in that format such as bioscope, SHRiMP and BWA. More information about the dibase ...
written 5.7 years ago by Gww2.6k
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Answer: A: Is There An Easy Way To Properly Orient Sequences For Clustalw Alignment?
... Perhaps you could build a small sequence database of known sequences and then align your queries sequences against the database to determine their orientation. You would need to choose an aligner with a suitable length for your queries but that shouldn't be hard to find. If the queries orientation ...
written 5.7 years ago by Gww2.6k
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Comment: C: Good Bioinformatics Library In C Similar To Biopython?
... I disagree that C++ is more complicated for memory management. They have all of the STL data structures plus destructors are automatically called when an object passes out of scope. With C you have to remember to free everything you allocate yourself. ...
written 5.8 years ago by Gww2.6k

Latest awards to Gww

Good Question 14 months ago, asked a question that was upvoted at least 5 times. For Simulating Rna-Seq Reads
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Weird Fastq Sequences
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Truncating Bam Files With Samtools
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: Weird Fastq Sequences
Commentator 3.2 years ago, created a comment with at least 3 up-votes. For C: Good Bioinformatics Library In C Similar To Biopython?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Weird Fastq Sequences
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Future Directions In Bioinformatics
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Which Dna Compression Algorithms Are Actually Used?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: What Does Bwa Expect In Its Alignment Database
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Truncating Bam Files With Samtools
Appreciated 3.5 years ago, created a post with more than 5 votes. For Simulating Rna-Seq Reads
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Counting Repeat And Unique Reads Of Tophat Output
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Is There Such A Thing As A Ucsc Api?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Recommend Your Favorite Bioinformatics Books
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Fundamentals Of Designing Biological Databases?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Are All Splice Site Regulatory Elements Within Their Target Gene?
Appreciated 3.5 years ago, created a post with more than 5 votes. For C: Code Golf: Best Dynamic Reverse Complement In Html/Javascript
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Truncating Bam Files With Samtools
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Why Are Sam/Bam Files So Large?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Raw Alignment Score Calculation
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Weird Fastq Sequences
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Weird Fastq Sequences
Good Answer 3.5 years ago, created an answer that was upvoted at least 5 times. For A: Counting Repeat And Unique Reads Of Tophat Output
Appreciated 3.5 years ago, created a post with more than 5 votes. For C: How To Efficiently Parse A Huge Fastq File?

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