User: Carlo Yague

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Carlo Yague4.3k
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Posts by Carlo Yague

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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 15 days ago by Carlo Yague4.3k
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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 22 days ago by Carlo Yague4.3k
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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 26 days ago by Carlo Yague4.3k
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Answer: A: Seeking ideas and guidance for an undergraduate project
... > Structure prediction (homology modelling/ab initio/threading) This is realistic. I have done something similar when I was undergraduate (my project was to design mutations that stabilizing two of the four structural configurations of a protein). However, its probably too ambitious to develop y ...
written 26 days ago by Carlo Yague4.3k
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Comment: C: hisa2 warning message dunring alignment of fasta file with reference genome
... Are you sure your command wasn't the following one? path/to/hisat2 -f -x /path/to/grch38/genome -1 path/to/SRR925687_1.fa -2 path/to/SRR925687_1.fa -S path/to/SRR925687.sam That would make more sense given the warning message. ...
written 26 days ago by Carlo Yague4.3k
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Comment: C: Proper design for DESeq2 and other RNAseq general questions
... Ok, now I understand why `tissue*tree` is not working. `tissue*tree` is equivalent to `tissue + tree + tissue:tree` (interaction). However, to be able to compute the interaction term, you would need at least two exact replicate of each (tissue-tree) couple. With your data, the best you can do is us ...
written 4 weeks ago by Carlo Yague4.3k
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Comment: C: Proper design for DESeq2 and other RNAseq general questions
... Could you paste your Design matrix ? From your post, it is unclear whether the samples came from the 3 (2) same trees or from 20 different trees. If they come from different trees, then, as h.mon suggested, you should only consider the "tissue" factor in your formula. ...
written 4 weeks ago by Carlo Yague4.3k
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Comment: C: RNAseq analysis with very close species
... Ok, its not that bad, but not so good either. Now it is up to you to decide: Is it ok to miss about 50% of information with option 3, knowing that the interpretation of the results will be simpler (you can easily compare differentially expressed genes from species 1 and 2) ? Or do you have the tim ...
written 4 weeks ago by Carlo Yague4.3k
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Comment: C: RNAseq analysis with very close species
... How close are the two species ? (% genome identity, etc) You can always try option 3, because it is the easiest, and see how it goes. If most of your reads are unmapped, then I'm afraid that you will have to use option 1 (or de novo transcriptomic assembly). ...
written 4 weeks ago by Carlo Yague4.3k
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Comment: C: Weird R behaviour with NAs in DESeq2 results
... Good catch ! Thanks ! ...
written 5 weeks ago by Carlo Yague4.3k

Latest awards to Carlo Yague

Commentator 26 days ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Scholar 6 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 7 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 10 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: The bed12 format
Scholar 5 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
Scholar 6 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 7 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 8 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 8 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 9 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 9 months ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq data.
Teacher 9 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 10 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 10 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 10 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 11 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

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