User: viktorfeketa

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Posts by viktorfeketa

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Comment: C: RNASeq alignment and quantification for a transgenic mouse
... In this case, the read counts for the transgene will include only a fraction of the total reads that actually came from the transgene (the rest of the reads aligning to the original gene) - thus, underestimated quantification. But now that I think about it, I could just add the read counts to both t ...
written 7 months ago by viktorfeketa0
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Comment: C: RNASeq alignment and quantification for a transgenic mouse
... 1) we are definitely interested in the whole transcriptome, but for this it seems to me that using the usual RNAseq pipeline with the original wild-type genome is sufficient - only the targeted gene will be affected, reads for all the other genes should be aligned/quantified normally - isn't that ri ...
written 7 months ago by viktorfeketa0
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Comment: C: RNASeq alignment and quantification for a transgenic mouse
... The concern that I have with this approach is that because the sequences are conserved to a large degree (the gene is the ortholog from a different organism), couldn't that result in some reads aligning (with imperfect alignment) to the original gene, and all reads being split between the original g ...
written 7 months ago by viktorfeketa0
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RNASeq alignment and quantification for a transgenic mouse
... I have RNASeq data coming from a transgenic mouse (where a single gene's coding sequence is replaced by the gene sequence from another organism). I need to quantify the expression of this transgene (get the number of aligned reads). It seems to me that the most comprehensive and accurate approach wo ...
transgenic mouse alignment rna-seq custom genome written 7 months ago by viktorfeketa0 • updated 7 months ago by swbarnes25.0k
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Inaccurate read counts when genome/annotation contains alternate loci
... I am performing gene quantification of the RNASeq data and getting very different read counts for one particular gene (most are very close) using two different reference genomes/annotations: NCBI and Gencode. I noticed that the annotation from NCBI contains two entries for this gene, one of them in ...
htseq-count star rna-seq alternative loci written 10 months ago by viktorfeketa0
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Comment: C: Split BAM file into parts with headers rebuilt
... the downstream tool that I am trying to use works by loading all contigs into memory. Because this particular input has too many contigs, the tool crashes due to prohibitively high memory usage. One solution that I was advised is to split the input BAM into parts, and include only a subset of contig ...
written 23 months ago by viktorfeketa0
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Split BAM file into parts with headers rebuilt
... Hi, I have a BAM file with 12000 contigs, I need to split it into several parts (let's say 12 parts with 1000 contigs each), and I also need the header to be rebuilt to include only the contigs relevant to this part. Could you please suggest a way to do that? ...
bam contigs rna-seq split written 23 months ago by viktorfeketa0

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