User: mlopez

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mlopez10
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1 year, 6 months ago
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1 year, 12 months ago
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Posts by mlopez

<prev • 7 results • page 1 of 1 • next >
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Comment: C: Abundance/frequency of RNASeq raw reads mapped to a transcript exon
... There is another person in the lab working with the same samples and that was her account. She is focusing more on the bioinformatic aspect and so I asked her to post the question originally. When I found out the sign up was free, then I posted the question. I apologize for any confusion I might hav ...
written 24 months ago by mlopez10
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Comment: C: Adding annotation into a transcript in order to use TopHat2
... We are working with doryteuthis pealeii. We are examining isoform properties one protein in 6 different muscles. There was a paper published containing loligo brachial heart muscle sequence and we used this as our first template to make primers for ours muscles of interest until we were able to sequ ...
written 24 months ago by mlopez10
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Comment: C: Adding annotation into a transcript in order to use TopHat2
... We also don't have a reference genome, would this cause any issues? Thank you ...
written 24 months ago by mlopez10
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Adding annotation into a transcript in order to use TopHat2
... Hello everyone, I am thinking about using TopHat2 to calculate the frequency/ abundance of RNA-Seq reads to 4 possible alternatively spliced exons. I have a cDNA composite that contains all the exon form each isoform but I don't know how to annotate the 4 I want to focus on so that I only get reads ...
rna-seq written 24 months ago by mlopez10
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Comment: C: Abundance/frequency of RNASeq raw reads mapped to a transcript exon
... I have exon sequences yes. ...
written 24 months ago by mlopez10
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HTSeq-count annotation and abundance count of exons from a cDNA composite
... We have 6 muscle types with 4 specific exons that look to be alternatively spliced are present in each muscle type. We have paired-end Illumina RNASeq reads and we are working with a non-model organism with no reference genome. We have a working composite for a protein sequence that includes every ...
rna-seq written 24 months ago by mlopez10
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Abundance/frequency of RNASeq raw reads mapped to a transcript exon
... We have paired-end Illumina RNASeq reads and we are working with a non-model organism with no reference genome. We have a working composite for a protein sequence that includes every exon we have found via cDNA. We have 6 muscle types with some triplicates and want to see how many times 4 specific e ...
rna-seq written 24 months ago by mlopez10 • updated 24 months ago by Devon Ryan96k

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