User: ruisergioluis

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Posts by ruisergioluis

<prev • 7 results • page 1 of 1 • next >
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Answer: A: How to obtain transcript level TPM using stringtie?
... 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 ruisergioluis20
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Comment: C: Direct cDNA nanopore strandness discover - 2D approach
... Thank you for your advice! ...
written 12 days ago by ruisergioluis20
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Comment: C: Direct cDNA nanopore strandness discover - 2D approach
... > 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 ruisergioluis20
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Answer: A: uploading bigwig file (converted from BED) to UCSC genome browser: Unrecognized
... 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 ruisergioluis20
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Comment: C: Direct cDNA nanopore strandness discover - 2D approach
... 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 ruisergioluis20
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Comment: C: Direct cDNA nanopore strandness discover - 2D approach
... 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 ruisergioluis20
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Direct cDNA nanopore strandness discover - 2D approach
... 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 ...
direct cdna long reads nanopore strand written 13 days ago by ruisergioluis20

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