User: dario.garvan

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dario.garvan420
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Australia
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Posts by dario.garvan

<prev • 58 results • page 1 of 6 • next >
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Comment: C: Efficent Estimation of Sequencing Coverage
... The percentage of reads aligned isn't output by `bwa mem` at the end of alignment process, unlike Bowtie 2, unfortunately. ...
written 9 days ago by dario.garvan420
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Efficent Estimation of Sequencing Coverage
... I am using [MELT][1], a tool which annoyingly requires the user to specify the [coverage of each BAM file as an input parameter][2]. > Please use a tool to determine approximate (+/- 2x) coverage prior to analysis. The data I have is whole genome sequencing data of 55 humans, which, based on f ...
samtools coverage written 9 days ago by dario.garvan420 • updated 9 days ago by harold.smith.tarheel4.3k
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Answer: A: Using expression array data to predict ethnicty
... It is possible. Any multi-class classification algorithm would be applicable, such as multinomial logistic regression or random forest. ...
written 12 months ago by dario.garvan420
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Comment: C: Retrieval of batch info for GSE46691
... No, the dataset consists of hundreds of microarrays, which were run at different times. Hence, batch effect correction is an important consideration for the analysis of them. ...
written 12 months ago by dario.garvan420
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Answer: A: Retrieval of batch info for GSE46691
... The submitter didn't provide the batch identifier of the batch each sample was run in, so it can't simply be downloaded from GEO Browser. It might be obtainable if you contact the corresponding author and ask for it. ...
written 12 months ago by dario.garvan420
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Comment: C: Using expression array data to predict ethnicty
... Why did you use the RNA-seq tag for your post if your question is about microarray data? ...
written 12 months ago by dario.garvan420
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Comment: C: Analyzing RNA-seq without replicates
... I have essentially the same characteristics in the dataset which I'm currently analysing. Using the different patients with the same clinical outcome as replicates doesn't work because there's a lot of heterogeneity between them, so no genes are found to be significantly differentially expressed. Th ...
written 12 months ago by dario.garvan420
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Comment: C: Duplicated Gene ID in gene_exp.diff file
... Cufflinks hasn't been updated in a couple of years and doesn't appear to be maintained. Do you really want to use it for your analysis? ...
written 12 months ago by dario.garvan420
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Answer: A: De novo RNA-seq
... The minimum contig length of 200 is used by most published research using Trinity. It's a simple filtering to avoid reporting numerous partial transcripts which are not likely to be long enough to code for a protein. I guess that the two exons which you designed for testing are both quite short. ...
written 12 months ago by dario.garvan420
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Comment: C: Number of mapped reads from BAM file
... The solution doesn't scale well for the situation when all alignments for a read are output and many reads have multiple valid alignments. Some tools, such as STAR, output text files of read mapping statistics, but others, such as Bowtie, don't save any such files and unfortunately require calculati ...
written 18 months ago by dario.garvan420

Latest awards to dario.garvan

Scholar 6 months ago, created an answer that has been accepted. For A: Pretty display of values for samples arranged in a 384-well plate (in R).
Popular Question 12 months ago, created a question with more than 1,000 views. For Unusual Cox Proportional Hazards Results for Highly Expressed Microarray Probes
Scholar 12 months ago, created an answer that has been accepted. For A: Pretty display of values for samples arranged in a 384-well plate (in R).
Scholar 23 months ago, created an answer that has been accepted. For A: Pretty display of values for samples arranged in a 384-well plate (in R).
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Large Tables In Supplementary Pdf In Journal Articles
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Fixing Encode Rna-Seq Fastq Files
Scholar 2.9 years ago, created an answer that has been accepted. For A: Pretty display of values for samples arranged in a 384-well plate (in R).
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: RNA-seq replicates pooled before sequencing. How to proceed with DGE analysis?
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Count 5'End Mapped To A Specific Genomic Position
Appreciated 4.5 years ago, created a post with more than 5 votes. For Large Tables In Supplementary Pdf In Journal Articles
Appreciated 4.9 years ago, created a post with more than 5 votes. For Large Tables In Supplementary Pdf In Journal Articles
Popular Question 4.9 years ago, created a question with more than 1,000 views. For Large Tables In Supplementary Pdf In Journal Articles
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Count 5'End Mapped To A Specific Genomic Position

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