User: dec986

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dec986100
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Posts by dec986

<prev • 89 results • page 1 of 9 • next >
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Comment: C: STAR Alignment Score reduced after trimming
... Is there any official documentation for this? I can't find anything in google searches or in the STAR manual ...
written 2 days ago by dec986100
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samtools stats typical ranges and explicit definitions
... hello, I am looking for more thorough documentation than what is provided for samtools stats http://www.htslib.org/doc/samtools.html because I have no idea what typical ranges are for lots of these values, specifically the ones that show up with "SN" For example, what is a good quality score? What ...
samtools rna-seq written 12 days ago by dec986100
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Measure Sequencing Depth in aligned BAM file
... I have some aligned BAM files and I want to calculate the sequencing depth, but numerous google searches have not produced any results. I could generate a tool by myself, but I want to use something which has been used by others so that there is less room for error. ...
rna-seq written 16 days ago by dec986100
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Meaning of Decimal points in ENST notation
... Hello, I have been seeing many transcripts that look like `ENST00000376701.4` and it matches an `ENSG...15285.10` my question is, What is the significance of numbers coming after the decimal point? Can they be safely ignored? I ask because I am giving a list of transcripts without the decimals i ...
rna-seq written 20 days ago by dec986100 • updated 20 days ago by goodez240
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Comment: C: Automating Gorilla And/Or Revigo Analysis
... this does not capture the Excel output. How can this be modified so the 3 excel files can be saved? ...
written 10 weeks ago by dec986100
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MSigDB gene set enrichment analysis
... Hello, I have been using Gorilla gene ontology with help from a great post on BioStars https://www.biostars.org/p/70064/ However, a colleague wishes to use 8 separate analyses listed on http://software.broadinstitute.org/gsea/msigdb/index.jsp for each comparison in our project I have a *lot* of a ...
gene ontology gsea written 3 months ago by dec986100
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Comment: C: [Opinion] - What alignment software do you use?
... For my particular purpose, I downloaded GSE96075 and compared STAR against HISAT2. STAR's extra reads could indeed be false positives, but I had no way of verifying that. I was satisfied because the read length was fairly long (~198 nucleotides) so the slightly higher mismatch mean was acceptable. ...
written 3 months ago by dec986100
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Answer: A: [Opinion] - What alignment software do you use?
... Through my own experimentation, STAR gives the best balance between selectivity and sensitivity. However, the mismatch rate is a little higher than HISAT2. I don't think that this is significant. HISAT2 comes as 2nd place, as it gets far fewer reads (sometimes tens of thousands with similar setti ...
written 3 months ago by dec986100
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Comment: C: Differentially methylated regions: Easy & Fast Identification and ANnoTation
... how do you mean 'truncated'? could you provide a specific example, so if something is wrong, I can fix it? ...
written 4 months ago by dec986100
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Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
... ## Introduction ## I would like to show how to use a new program to identify differentially methylated regions (DMRs) from bisulfite sequencing data, whether whole-genome or RRBS. This tutorial won't be very long, as the program is remarkably easy to use, and doesn't require learning a programming ...
dna methylation tutorial dmr written 4 months ago by dec986100

Latest awards to dec986

Popular Question 10 weeks ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: [Opinion] - What alignment software do you use?
Popular Question 4 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 4 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 5 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 6 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Scholar 8 months ago, created an answer that has been accepted. For A: Alignment with STAR produces unique bam files, but identical output from bedtool
Popular Question 15 months ago, created a question with more than 1,000 views. For Installation of Bcl2Fastq Fails
Popular Question 15 months ago, created a question with more than 1,000 views. For R programming: Keep Heatmap Items Within Image Frame
Popular Question 15 months ago, created a question with more than 1,000 views. For Conversion between .bedGraph or .bw to 7-column format
Popular Question 15 months ago, created a question with more than 1,000 views. For edgeR: no residual df: Cannot estimate dispersion
Supporter 15 months ago, voted at least 25 times.
Popular Question 20 months ago, created a question with more than 1,000 views. For DESeq2 comparison failure
Scholar 2.2 years ago, created an answer that has been accepted. For A: Alignment with STAR produces unique bam files, but identical output from bedtool

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