User: Ruixuan

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Ruixuan0
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Posts by Ruixuan

<prev • 14 results • page 1 of 2 • next >
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Comment: C: How to convert gff3 format, PASApipeline
... Thank you so much!!!! ...
written 10 days ago by Ruixuan0
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Comment: C: How to convert gff3 format, PASApipeline
... Cross-post at reddit: https://www.reddit.com/r/bioinformatics/comments/lpjmp5/how_to_convert_gff3_format_pasapipeline/ ...
written 11 days ago by Ruixuan0
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How to convert gff3 format, PASApipeline
... Hi all, I'm doing UTR annotation with the use of PASA. Refer to [https://github.com/PASApipeline/PASApipeline/wiki/PASA\_genome\_annotation](https://github.com/PASApipeline/PASApipeline/wiki/PASA_genome_annotation). A gff3 file is needed in this process. The sample gff3 it provides is like g ...
assembly rna-seq written 11 days ago by Ruixuan0 • updated 11 days ago by Juke345.2k
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Comment: C: Extract primer-containing reads from RNA-Seq
... Thanks for the reply. I also noticed this and cannot find any sequence of their primer. So I turned to Trinity and PASA for border annotation. If you have any advice, I'm looking forward to that. Thanks again. ...
written 3 months ago by Ruixuan0
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Comment: C: Extract primer-containing reads from RNA-Seq
... Thank you very much! ...
written 3 months ago by Ruixuan0
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Extract primer-containing reads from RNA-Seq
... Hi all, I was wondering if there are any methods to extract reads containing the primer sequence. My goal is to identify the transcript borders from reads, thus, I think if I could collect reads with primer mark, then these reads could represent the border part of transcripts. Then, mapping them ...
rna-seq written 3 months ago by Ruixuan0 • updated 3 months ago by swbarnes29.6k
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Comment: C: How to identify mRNA 3' UTR by bulk RNA-seq data
... Thank you! I'll check it. ...
written 4 months ago by Ruixuan0
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Comment: C: How to identify mRNA 3' UTR by bulk RNA-seq data
... Thank you for your reply. But sadly there is no reference annotation for 5' and 3' UTRs, there is only CDS information. :( ...
written 4 months ago by Ruixuan0
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How to identify mRNA 3' UTR by bulk RNA-seq data
... Hi there, I was wondering if there are any tools that can identify mRNA 3' end and also 5' end by bulk RNA-seq data. My goal is to determine the transcription start site and the transcription termination site. I think maybe extracting mapping information from BAM file maybe an approach? But I'm n ...
rna-seq written 4 months ago by Ruixuan0 • updated 4 months ago by A. Domingues2.4k
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Find motifs relative location to features
... Hi there, Before I used MEME to search the upstream of genes aiming to look for any motifs. Now, I'm using motifs from MEME and use FIMO to scan through the genome to find whether there are other locations of these motifs. I got a tsv file from the FIMO, which contains `motif_id | motif_alt_id ...
fimo meme motif written 4 months ago by Ruixuan0

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