User: standonn

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standonn0
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Posts by standonn

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Comment: C: Variant calling within and between 2 nematode strains
... Thanks a lot for your answer! The links you sent really do help! ...
written 14 months ago by standonn0
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Variant calling within and between 2 nematode strains
... Dear all, I have the genome sequence of a nematode species I'm working with. This genome was assembled using reads (3 pair-end libraries and 2 mate-pair) from one particular strain (let's call it Strain A). Now I have one pair-end library for another strain (Strain B). I would like to call SNPs ...
reads reference genome snp written 14 months ago by standonn0 • updated 14 months ago by Medhat7.1k
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Comment: C: Combining de novo and genome guided transcriptome assembly for expression analys
... Thanks for your answer! It does help. Yes I do have good quality PE reads. So if I understand correctly I would build several transcriptome assemblies, using different programs (Trinity, Cufflinks) and different strategies (de novo and genome-guided), merge them and use EvidentialGene/tr2aacds.pl to ...
written 20 months ago by standonn0
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Combining de novo and genome guided transcriptome assembly for expression analysis?
... Dear all, I am about to do some RNA-seq analysis to find differently expressed (DE) genes between different conditions. I am studying a nematode which is relatively unknown but for which I have a genome assembled (not published yet). Now because I have a genome I could use the tuxedo pipeline (t ...
de novo expression analysis rna-seq genome-guided written 20 months ago by standonn0 • updated 20 months ago by gilbert.bionet110

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