User: Carlo Yague

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Carlo Yague4.4k
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Posts by Carlo Yague

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Comment: C: featureCounts strand specificity
... If you want to count on both strand, use -s 0 (which is the default behaviour). ...
written 11 weeks ago by Carlo Yague4.4k
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Comment: C: weird number in log2FC
... Did you use excel at some point in your analysis ? Its automatic formating can be a pain sometimes. PS: I think your question lacks some context. Where does your data come from ? And what have you done with it to obtain those numbers ? ...
written 3 months ago by Carlo Yague4.4k
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Answer: A: Antisense transcription from strand specific RNA-seq
... > I want to detect sense and antisense transcription of each gene. To do that, you don't actually have to split your bam into fwd and reverse and I think that what you are trying to do in your answer is overly complicated. An approach I used with success is to simply count the reads mapping in f ...
written 3 months ago by Carlo Yague4.4k
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Comment: C: Extract sequences from a FASTA file using a gtf file
... Love the comments xD ...
written 3 months ago by Carlo Yague4.4k
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Answer: A: Extract sequences from a FASTA file using a gtf file
... 1. Pull only the transcripts listed in the gtf file from the FASTA file Use [bedtools getfasta][1]. 2. Find the longest ORFs See this [related thread][1] for some options. [1]: https://www.biostars.org/p/104936/ ...
written 3 months ago by Carlo Yague4.4k
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Comment: C: Orientation of PE reads a review of --fr --ff and --rf meanings
... Yes, what I actually meant is that you will not (usually) reverse-transcribe the full mRNA from the 5' end to the 3' end. So sometimes you will have the poly-A in your fragment, but not always. This is much clearer in the revision now. ...
written 3 months ago by Carlo Yague4.4k
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Comment: C: Orientation of PE reads a review of --fr --ff and --rf meanings
... This is a nice summary. Here are a few suggestions: - This is not really a "question", it could be more appropriate to flag this post as "forum". - You should export your powerpoint as image instead of using snapshots because we can see the auto-spelling-mistake-detection with the red waves under ...
written 3 months ago by Carlo Yague4.4k
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Comment: C: Using samtools sort to convert .sam files to .bam files
... Note that if what you are really after is sam - bam conversion, its must faster to use `samtools view` (but it doesn't sort obviously). ...
written 4 months ago by Carlo Yague4.4k
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Comment: C: Compatibility between my reference genome and GTF file
... The "tran" versions of the indexed genomes on the [HISAT2 website][1] contains the GTF annotation files. Its probably easier to use these. [Link to download GRCh38 index + GTF][2]. [1]: https://ccb.jhu.edu/software/hisat2/manual.shtml [2]: ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/data/grch38_ ...
written 4 months ago by Carlo Yague4.4k
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Comment: C: hisa2 warning message dunring alignment of fasta file with reference genome
... That's weird... it might be bug then, although I don't known for sure. The code responsible for that warning in hisat2: // Check for duplicate mate input files if(format != CMDLINE) { for(size_t i = 0; i < mates1.size(); i++) { for(size_t j = 0; j < mates2.size(); j++) { ...
written 4 months ago by Carlo Yague4.4k

Latest awards to Carlo Yague

Teacher 27 days ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: DESeq2 input for DE analysis
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Scholar 5 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 5 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 6 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 6 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 6 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: The bed12 format
Scholar 9 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 10 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Scholar 10 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 12 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 13 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 13 months ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq data.
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 14 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

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