User: corend

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corend50
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Posts by corend

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Comment: C: RNAseq analysis with very close species
... I edited my post, I align 47% of reads from species 2 on the genome of my first species. ...
written 1 day ago by corend50
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Comment: C: RNAseq analysis with very close species
... I am aligning on the "good" genome to see if the percentage of uniquely mapped reads is ok. ...
written 1 day ago by corend50
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Comment: C: RNAseq analysis with very close species
... I could add this idea to the previous list, but would it be better and why? ...
written 1 day ago by corend50
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RNAseq analysis with very close species
... I am currently working on a RNAseq data set from 2 conditions in 1 species. For this species the genome is nice (I have full chromosomes) and well annotated. I used the [`New tuxedo`][1] pipeline to analyse my results. This worked very well. I now retrieved some RNAseq data from a very close specie ...
rna-seq written 2 days ago by corend50
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Comment: C: Hisat2 multimapped reads
... > Just because one read of a pair can theoretically map to multiple > places doesn't mean that the fragment can map to multiple places. Exactly that is what I want to dodge. If a fragment has two alignments with good MAPQ, filtering by MAPQ will make me keep the pair when I don't want it no ...
written 8 weeks ago by corend50
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Comment: C: Hisat2 multimapped reads
... In that case, I get rid of pairs mapping concordantly once with one read of the pair with multiple alignments ? If a pair has only one concordant mapping I would like to keep it even if one of the read maps somewhere else also. ...
written 8 weeks ago by corend50
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Hisat2 multimapped reads
... I work with paired RNA-seq data from 2 conditions in 1 species. I aligned those data on the reference genome using `hisat2`. I am interested on retrieving reads concordantly mapped only once in the genome. I filtered the SAM output using [this post][1], but here is the problem : They say that `ZS ...
alignment rna-seq hisat2 written 8 weeks ago by corend50 • updated 8 weeks ago by Devon Ryan84k
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Comment: C: Ballgown finds few DE genes compared to DESeq
... Thanks a lot, I will keep using DESeq2 for DE analysis and use Ballgown to have an idea of gene expression level in FPKM. You can switch this to an answer! ...
written 10 weeks ago by corend50
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Comment: C: Ballgown finds few DE genes compared to DESeq
... I am not sure to understand what do you mean with > may be sing FPKM data when conducting the differential expression > analysis I used this command line in ballgown: results_genes = stattest(bg, feature="gene", covariate="Tissue", getFC=TRUE, ...
written 10 weeks ago by corend50
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Comment: C: Ballgown finds few DE genes compared to DESeq
... I agree for point 1), but even if the statistical methods are different I expect approximately the same results no ? For point 2) I edit my post thanks ! ...
written 11 weeks ago by corend50

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