User: freuv

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freuv20
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Posts by freuv

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Comment: C: Unknown Stringtie IDs produced when using Ensembl GTF
... stringtie aligned.bam -v -o output.gtf -p 12 -G Mus_musculus.GRCm38.92.gtf -A abundance.txt -C fully_covered_refs.txt ...
written 8 weeks ago by freuv20
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Comment: C: Unknown Stringtie IDs produced when using Ensembl GTF
... They are not MSTRG tags -- they are formatted as STRG.nnnn ...
written 8 weeks ago by freuv20
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Comment: C: Unknown Stringtie IDs produced when using Ensembl GTF
... Thank you! I will be sure to do this going forward. ...
written 8 weeks ago by freuv20
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Comment: C: Help interpreting Stringtie 'fully covered transcripts' output
... Would this suggest that there are alternatively spliced transcripts of the same gene present? ...
written 8 weeks ago by freuv20
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Help interpreting Stringtie 'fully covered transcripts' output
... I ran Stringtie on RNASEQ data with the -c option, which produces a list of reference genes that are covered end-to-end by reads from your run. However, I am having some difficulty interpreting the output. Specifically, there are multiple entries for the same Ensembl ref annotation and I'm not sur ...
assembly rna-seq written 8 weeks ago by freuv20
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Unknown Stringtie IDs produced when using Ensembl GTF
... I quantified gene expression using an Ensembl GTF as a reference. However, the abundance estimates contain several thousand Stringtie IDs in addition to the Ensembl IDs. Where did Stringtie pull these IDs from? How can they be converted to a more common identifier? ...
gtf ensembl stringtie rna-seq written 8 weeks ago by freuv20 • updated 8 weeks ago by Emily_Ensembl15k
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RSeQC python runtime errors for tin.py
... Hello, I am attempting to use the tin.py script in the RSeQC package, on BAM files generated by STAR aligner. When running tin.py, I end up with the following error: /python-2.7.15/lib/python2.7/site-packages/numpy/core/fromnumeric.py:2957: RuntimeWarning: Mean of empty slice. out=out, ...
software error rna-seq sequencing written 10 weeks ago by freuv20 • updated 10 weeks ago by WouterDeCoster31k
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Comment: C: determining cutoff for Kaplan Meier
... Which is more suitable for TCGA data where you don't really have control over the number of patients that fall into each quartile/cut-point bin? ...
written 6 months ago by freuv20
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Comment: C: Survival analysis in R using maxstat package -- clarification needed on methodol
... Hi arta, thank you for your quick response. If I am understanding correctly, are they not two different approaches? In the maxstat approach, we divide all patients within the 10-90% percentile of gene expression by a single cut-point value. What is above that is 'high' expression and what is below ...
written 6 months ago by freuv20
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Comment: C: Survival analysis in R using maxstat package -- clarification needed on methodol
... Why should one use a cut-point to classify 'high' and 'low' expression versus, say, selecting the patients with the top 10% highest expression and lowest 10% expression as your 'high' and 'low' cohort? ...
written 6 months ago by freuv20

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