User: Ekarl2
Ekarl2 • 90
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Posts by Ekarl2
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... I have a species that has a 4-5% variation between alleles and each RNA-seq sample has several hundreds individuals. I am mapping against a template from another, single individual that has a much more complete transcriptome assembly.
Currently, I am using bowtie + RSEM, but the way bowtie works se ...
written 3.5 years ago by
Ekarl2 • 90
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... 1. I do not have the RSEM mapping .bam at the moment (removed it due to storage issues), but I quickly ran a everything-default bwa mapping with the assembly reads against just the clones. This showed a substantial amount of mapping (in accordance with expectations), but with lots of SNPs across re ...
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... Well, at the moment we know the clone is a true CDS and we also have functional studies supporting homology above and beyond sequence similarity for some of the sequences of interests. Thank you for your efforts, but I do not think this exchange relates to my mapping question anymore.
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written 3.6 years ago by
Ekarl2 • 90
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... You take a reference sequence from a nearby species. You BLAST this sequence against the assembly. You pick up the 2-3 fragments that together match the vast majority of query sequence in a convincing way (with support from e. g. domain searchers and phylogeny). You make a construct from these 2-3 f ...
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... Put together the fragments (identified by BLAST with a homolog from another species as a query) into a construct, make PCR primers from construct, run PCR, sequence results.
...
written 3.6 years ago by
Ekarl2 • 90
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... I have an RNA-seq assembly and the corresponding reads form a non-model organism. Those reads map (using RSEM with bowtie via a Trinity wrapper) well against the assembly generally and transcripts of special interest.
However, the subset of transcripts in question that I am very interested in are s ...
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... I have an RNA-seq dataset with two treatments (A and B) and four environments in a classic +/+, +/-, -/+, -/- design with four replicates for environment for a total of 16 samples. There are also four batches: 1 replicate of each environment occurs in the first batch, 2 replicate of each environment ...
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... I have an RNA-seq dataset that have been batch-corrected for the purpose of making a heatmap to look at in a paper. For the differential expression analysis, I added the batch effect as an element in the design matrix in EdgeR. Here I am just interested in visualization.
The R script that I have be ...
written 3.7 years ago by
Ekarl2 • 90
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Comment:
C: Can FPKM be added?
... This was very helpful! Does the information you mentioned above also apply to cases were I would like to combine FPKM for two separate paralogs too where both are full length (say 2000 nt)? In those cases, I do not see an intuitive way to calculate a new combined length. Would I just divide the comb ...
written 3.9 years ago by
Ekarl2 • 90
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... Hi,
I have an de novo RNA-seq dataset that I have run RSEM on the gene-level and gotten out FPKM for all Trinity genes in the assembly. Unfortunately, the assembler split up a real gene (say, a transporter) into two separate Trinity genes in the assembly, so the first Trinity gene contains the firs ...
written 3.9 years ago by
Ekarl2 • 90
• updated
3.9 years ago by
michael.ante • 3.4k
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For How to handle Trinity post-filtering singletons from paired-end sequencing?
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4.2 years ago,
created a question with more than 1,000 views.
For RNA-seq, EdgeR and batch effects
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