User: jnoble333

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jnoble33320
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Posts by jnoble333

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Answer: A: Prediction of TSS from tuxedo pipeline
... I think in the case of a + strand transcript your TSS would be the leftmost position in exon 1 of the transcripts in the gtf file generated by cufflinks. ...
written 19 months ago by jnoble33320
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Answer: A: Best splicing variant
... What do you mean by best? Would it be the most highly expressed variant? It really comes down to what question you are trying to answer with your data set. ...
written 19 months ago by jnoble33320
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Comment: C: Mapping RNA-Seq data on genome from another species
... That is the post I went by. That threshold works for my dataset for the most part because I have a lot of reads. I'd say try different values and see how your results differ. ...
written 19 months ago by jnoble33320
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Answer: A: Mapping RNA-Seq data on genome from another species
... Hi tlorin, I use STAR to do this frequently with the parameter --outFilterMismatchNmax 8. You can check the alignment percentage in the Log.final.out file and adjust your mismatch threshold accordingly. You may face the issue of reads aligning to a lot of different locations and can filer your bam ...
written 19 months ago by jnoble33320
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Answer: A: RNA-seq analysis with quantitative traits
... Hey Javier, There isn't much work that has been done regressing the transcriptome onto quantitative phenotypic traits. I am attempting to do this as a component of my thesis. Here's a little insight I can provide: Differential expression packages like EdgeR, DeSeq, et al. will not be suitable for ...
written 19 months ago by jnoble33320
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Comment: C: Cuffcompare combined.gtf output contains only exons
... It follows the formate of transcript, exon, exon.... transcript (repeat). It definitely isn't the same as a reference annotation. It does not include a gene field. ...
written 2.4 years ago by jnoble33320
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Comment: C: Cuffcompare combined.gtf output contains only exons
... I was expecting the merge and compare output gtf's to follow the same format as a cufflinks output gtf, similar to the input gtf files. I do see your point about the redundancy though. My transcriptome assembly was genome guided. I'll give gtf2gtf a try to get the transcript lines added. Thanks! ...
written 2.4 years ago by jnoble33320
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Comment: A: Cuffcompare combined.gtf output contains only exons
... This also occurs when using cuffmerge on all of the gtf files. ...
written 2.4 years ago by jnoble33320
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Cuffcompare combined.gtf output contains only exons
... Hello, I have gtf files from a pasa run for 96 samples. My intention was to run cuffcompare on all 96 to produce a master gtf file for all samples. Instead when I run it my results contain only transfrags annotated as "exon". My organism is P. trichocarpa. I am calling cuff compare via: cuffcompar ...
rna-seq written 2.4 years ago by jnoble33320

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