User: bagi.m

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bagi.m10
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Posts by bagi.m

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Are there any tools for transcriptome reassembly and/or tailoring existing reference transcriptome to specific population?
... I have downloaded high quality (made from both long 454 and short reads) reference transciptome for my species from population A. I also have illumina reads from my experiment (few replicates, some treatments and control) all done in population B. I aligned the reads to the reference with bwa-mem. ...
assembly rna-seq written 10 months ago by bagi.m10 • updated 8 months ago by Biostar ♦♦ 20
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Comment: C: Why is eXpress producing strangely low counts?
... Thank you for your answer. I am indeed planing to try Salmon with this data, and see if I get to similar conclusion. I found some articles / posts claiming pseudoalignment tools are better, but both were based on human data. So I don't know if this claim holds for organisms with much higher intrasp ...
written 16 months ago by bagi.m10
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Answer: A: Why is eXpress producing strangely low counts?
... Ok, this one is embarrassing. I completely misunderstood the eXpress documentation regarding sorting the input .bam file and the fact that you are _not_ supposed to sort it. ...
written 16 months ago by bagi.m10
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Why is eXpress producing strangely low counts?
... I have aligned our RNA-seq to reference transcriptome (there is no genome) using bwa mem. The reference transcriptome is from the same species but from different population, so some mismatches and indels are expected. Then I used eXpress to count reads. The results are strangely low. No reference ...
rna-seq written 16 months ago by bagi.m10

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Scholar 16 months ago, created an answer that has been accepted. For A: Why is eXpress producing strangely low counts?

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