User: Sammy

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Sammy0
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Posts by Sammy

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Comment: C: GSM records without a corresponding SRA
... No, there are raw data available in the GSM. I am looking for RNA-seq from the 3rd party to process. Sometimes the SRP series is not as easy to find but I get it most of the times. The thing is that I upload the samples directly into Galaxy with the SRP. I don't really know what to do just with the ...
written 5 days ago by Sammy0
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GSM records without a corresponding SRA
... Hey, By your knowledge, is there possible for GSM records to not have a corresponding SRA page? ...
rna-seq written 5 days ago by Sammy0
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(Closed) TopHat and HISAT2
... Hey, all. Why TopHat gives totally different alignments when I change the Library Type (First strand vs. Second strand) and for HISAT2 the alignments are pretty much the same (Reverse vs. Forward). I am trying to read the papers that describes them but so far, couldn't explain this. I am aware of ...
rna-seq written 5 weeks ago by Sammy0
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Comment: C: Hisat2 vs. TopHat vs.Bowtie2
... Got it. Just to make sure for future references because I am new here and I kind of training myself in bioinformatics talking with very few people about it (so I really have to learn the terminology better): I am using Galaxy. Should I specify the function used and the chosen option? I am not sure a ...
written 6 weeks ago by Sammy0
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Comment: C: Library Types in TopHat and Hisat2
... Great. Thanks. So what you are saying is that I should not take the results from TopHat into consideration. ...
written 6 weeks ago by Sammy0
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Library Types in TopHat and Hisat2
... Hey, Does anyone know how to explain the background process on how spliced aligners (Hisat2, TopHat) use Library Types (Second Strand/ First Strand, Forward/Reverse respectively) to align the reads to the genome? More specifically, how Library Types influence the alignment. I am trying to understa ...
rna-seq written 6 weeks ago by Sammy0
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Comment: C: Hisat2 vs. TopHat vs.Bowtie2
... Right, but what about TopHat and Hisat2. Why Hisat2 gives me exons that are that long in comparison to TopHat when I introduce the same Library Type as an options (well, in this case the equivalent). I should add that I get long exons in TopHat as well but when I choose First Strand or Unstranded an ...
written 6 weeks ago by Sammy0
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Comment: C: Merging SAM/BAM files
... Huh. Probably because I don't think I know what you mean by that. Can you please give me more details? I am intrigued. ...
written 6 weeks ago by Sammy0
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Hisat2 vs. TopHat vs.Bowtie2
... Hey. On the same paired-end sample I used (in Galaxy) TopHat (FR-Second strand) and Hisat2 (fr; Reverse). After that I used "Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region" function to cut a region of 20 kb and visualise it in IGV. The thing that puzzles me is that I hav ...
rna-seq written 6 weeks ago by Sammy0
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Comment: C: Merging SAM/BAM files
... Because multiple alignments, multiple BAMs? No more questions. Thanks for your help. ...
written 6 weeks ago by Sammy0

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