User: Beginner

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Beginner30
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Posts by Beginner

<prev • 16 results • page 1 of 2 • next >
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Answer: C: Is it okay to use a ENSEMBL toplevel genome for mapping when no primary assembly
... I just found the answer. In an information file it says "If the primary assembly file is not present, that indicates that there are no haplotype/patch regions, and the 'toplevel' file is equivalent." indicating that the toplevel for rat is equivalent to a primary assembly version of other species su ...
written 11 days ago by Beginner30
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Is it okay to use a ENSEMBL toplevel genome for mapping when no primary assembly is available?
... Hi, I used to work with ENSEMBL genomes for differential gene expression. A new dataset is now in a species (rat) that does not have a primary assembly file, only toplevel. I normally used the primary assembly. I think it is fine, but just wanted to make sure that there won't be any major issues f ...
genome ensembl written 11 days ago by Beginner30
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Comment: C: Why and how to discard mapped reads based on strandedness?
... Do you know why someone would discard those reads? Is the reason why they choose to discard Ribo-Seq reads mapping to the second-strand and for the RNA-Seq dataset reads mapping to the first-strand because the "normal non-anti-sense" read of RNA-Seq should be reverse? And a normal Ribo-Seq read will ...
written 11 days ago by Beginner30
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Why and how to discard mapped reads based on strandedness?
... Hi, how can someone filter out reads based on the library strandedness? In a Ribo-Seq analysis, the Ribo-Seq reads mapping to the second-strand and for the RNA-Seq dataset reads mapping to the first-strand were discarded. **Why** would someone do this and **how** to do it (aligner was STAR). Than ...
ribosome profiling strandedness rna-seq written 12 days ago by Beginner30 • updated 12 days ago by swbarnes26.5k
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Comment: C: Probably very simple question for gffread
... Thank you for the fast answer! I think the spaced arose from a copy past issue and I corrected it. Do you know why this was done? Why would you collapse the "fully contained shorter coding sequences" of the GTF file and exlude the non-coding regions? ...
written 12 days ago by Beginner30
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Probably very simple question for gffread
... Hi everyone, I need to re-analyze some old data with a previous protocol that is not easily understandable as a beginner. In it it says: "We used the EnsEMBL mouse genome assembly GRCm38.p6, where all non- coding regions were excluded, and all fully contained shorter coding sequences were collapsed ...
gffread written 12 days ago by Beginner30 • updated 12 days ago by Dave Carlson120
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Answer: A: rRNA and tRNA removal from mouse Ribosome profiling data - getting correct seque
... Maybe there is any other suggestion, especially regarding the sources (and possible differences) for rRNA, tRNA, soRNA or other RNA species? ...
written 4 months ago by Beginner30
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Comment: C: rRNA and tRNA removal from mouse Ribosome profiling data - getting correct seque
... Sorry for my delayed answer. Thank you for your suggestion and I will try this. Still I am not sure about the differences in "complete repeating unit of Mus musculus ribosomal DNA" and the Silva rRNA database. E.g. does the "complete repeating unit of Mus musculus ribosomal DNA" contain the 5S rRNA? ...
written 4 months ago by Beginner30
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rRNA and tRNA removal from mouse Ribosome profiling data - getting correct sequences
... Hi, I need to filter rRNA and tRNA from a mouse ribosomal profiling and RNA seq datasets. Am I right with the assumption that since for mouse there exists the "complete repeating unit of Mus musculus ribosomal DNA" as found here, (https://www.ncbi.nlm.nih.gov/nuccore/BK000964), I can simply downloa ...
rrna ribosome profiling trna ribo-seq written 4 months ago by Beginner30
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Comment: C: How to filter sequencing reads in a fastq file by size?
... I tried it and it worked. Thank you for your help! ...
written 5 months ago by Beginner30

Latest awards to Beginner

Teacher 11 days ago, created an answer with at least 3 up-votes. For C: Is it okay to use a ENSEMBL toplevel genome for mapping when no primary assembly

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