User: plberry

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plberry30
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30
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New User
Location:
Kansas City, Missouri, USA
Last seen:
11 hours ago
Joined:
10 months, 3 weeks ago
Email:
p************@gmail.com

Posts by plberry

<prev • 16 results • page 1 of 2 • next >
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Answer: A: FASTQC: overrepresented sequences
... CutAdapt by default leaves the sequence IDs and blank lines for the base-call/quality scores in the output, even if all of the bases have been removed. You can alter this behavior by using `-m [minimum number of bases]` when you run CutAdapt. https://cutadapt.readthedocs.io/en/stable/guide.html#filt ...
written 11 hours ago by plberry30
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Comment: C: Identifying reading frame for Ribo-Seq reads
... These are ribo-seq reads, so the read lengths are only as long as a ribosome is wide, about 15-30 nts. Usually I would do the stop codon trick! I guess the main thing is that the rest of my analysis script is in Python and Python is so slow for anything where you have to read through files line by l ...
written 26 days ago by plberry30
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Identifying reading frame for Ribo-Seq reads
... I am trying to identify the A-site bound codons for a Ribo-Seq dataset. I know the A-site offsets for the three reading frames for the various lengths of reads, but I am puzzled about which reading frame to pick for each read. I can of course manually do this by getting the coding sequence for the g ...
ribo-seq a-site rna-seq written 27 days ago by plberry30 • updated 27 days ago by Mensur Dlakic9.2k
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Comment: C: Normalizing RNA-seq read counts within a single sample - gut check
... Reading through the Salmon documentation, it seems like I can run my already transcriptome-mapped reads through it - since I am going to be using the actual sequences of the ribosome footprints from the Ribo-seq analysis for some molecular-level dynamics analysis, will that avoid potential problems ...
written 5 weeks ago by plberry30
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Comment: C: Normalizing RNA-seq read counts within a single sample - gut check
... Apologies, "TI" should be "TR". TE is translational efficiency, which I learned as rpkM (sub in the updated normalization scheme) from your Ribo-seq data / rpkM from your mRNA-seq data. It should show the ratio of how many ribosomes are actually bound to a transcript. So if you have a highly transc ...
written 5 weeks ago by plberry30
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Normalizing RNA-seq read counts within a single sample - gut check
... I'm doing a pilot analysis on some public RNA-seq datasets that include mRNA-seq, Ribo-seq, and RNC-seq for the same samples. The analysis is part of a larger project to look at ways to predict protein structure/function/class by examining translational dynamics and seeing what they have in common. ...
rna-seq written 5 weeks ago by plberry30 • updated 5 weeks ago by rpolicastro4.1k
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Comment: C: Creating a non-coding RNA index for STAR
... Marking this as the answer - it took a little work to get BBmap up and running due to some dependencies permissions but it was 2 hours well spent! Worked a treat, definitely going to use this again when I need a quick and dirty way to separate out reads from large alignments. It churned through over ...
written 6 weeks ago by plberry30
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Comment: C: Creating a non-coding RNA index for STAR
... No, I need sequence and codon resolution, not just counts. I'm identifying exactly which codons the A and P sites are bound to. ...
written 6 weeks ago by plberry30
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Comment: C: Creating a non-coding RNA index for STAR
... I am using raw public RNC-seq, mRNA-seq, and Ribo-seq datasets to explore sequence and codon choice effect on protein phase separation behavior. In the lab we've observed some differences in phase-separation behavior that seem to be related which codons are used for the same amino acid. It makes no ...
written 6 weeks ago by plberry30
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Comment: C: Creating a non-coding RNA index for STAR
... Thanks for the tip on the BBMap suite, that looks very promising. ...
written 6 weeks ago by plberry30

Latest awards to plberry

Scholar 6 weeks ago, created an answer that has been accepted. For C: Finding sets of Ribo-Seq, mRNA-Seq, and RNC-Seq data

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