User: ruisergioluis
ruisergioluis • 20
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Posts by ruisergioluis
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... The TPMs values are located in the GTF file, returned by StringTie.
If you want a simple two-column file with Transcript ID and TPM, you can simply run the following command:
grep -P "\ttranscript\t" StringTie_sampleName.gtf | cut -f9 | awk '{gsub("\"","",$0);gsub(";","",$0);print $4,$12}'
I ...
written 5 days ago by
ruisergioluis • 20
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... Thank you for your advice! ...
written 12 days ago by
ruisergioluis • 20
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... > Could it be 1D^2 data?
Is this the latest cDNA PCR-free nanopore protocol?
For the 1D², is expected to find out the "mirror reads"? (even for a wrongly performed basecalling step) ...
written 12 days ago by
ruisergioluis • 20
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... That is a problem that I faced some time ago. I consider UCSC genome browser a fundamental and central tool for data visualization that can have a strong impact on the final analysis result.
However, I realized that I spent a lot of time preparing the side files to be interpreted by genome browser, ...
written 13 days ago by
ruisergioluis • 20
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... Thank you so much for your answer. It helped a lot to direct my attentions.
The data was produced using the most recent protocol. So, it is probably my completely fault. Right now I am working with the basecalled files sent by the facility. But, having into account what you said, I think I should ...
written 13 days ago by
ruisergioluis • 20
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... Thank you for your comment!
Correct me please if I'm wrong, but a 2D read is one that has cDNA double strand with a hairpin making the ligation between them in one of the sides. So, if the majority of my reads start with TTTTT and end with AAAAA, and the reads look a mirror (the sequence until the m ...
written 13 days ago by
ruisergioluis • 20
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... I have recently started working with RNA nonopore MinIon long reads. However, at the moment I have more doubts than answers.
From my (weak) understanding, there are 2/3 main approaches regardless to RNA nanopore miniIon:
1. direct RNA
2. direct cDNA (PCR-free)
3. cDNA (with a PCR step)
The da ...
written 13 days ago by
ruisergioluis • 20
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