Tang JIWEI

Hi, @arzwa Can the input sequence file of WGD use protein sequence directly or Pacbio full-length transcriptome sequence? Thank you！

Is Bambu suitable for PB Kinnex?

2

Hi, @andredsim Pacbio Kinnex full-length RNA now also supports isoform quantification, does Bambu plan to adapt it for this method?

Hi, @davidemms @robsyme @Neato-Nick OrthoFinder can detect orthologous genes from two species. I currently have the full-length transcript of Pacbio. Can I use this software to detect Orthologous Isoforms? Best!

Hi, @jebrosen **What do you want to know?** First, In some articles, I saw running RepeatMasker with transcriptome. Is this approach feasible? Second, There is no cotton species in the...

Is it possible to obtain the cds sequence?

5

Hi, @apcamargo Hello, the results I ran here only have protein sequences and no cds sequences. Can this software get the corresponding cds sequence codes?

Hi, @daler If converting bam for sashimiplot RNA-seq of alternative splicing to bigwig, should normalization be used, and if so, which one?

An error was found in the generated protein sequence

2

Hi @alephreish @gpertea I extracted CDS sequences and protein sequences based on the CDS contained in the GTF. `gffread Y2.gtf -g Genome.fa -x cds.fa -y pep.fa` But I found the...

Hi @gpertea @smoe I used the above command to merge two GTF files, which were constructed by PacBio to represent full-length isoforms `stringtie --merge -G Ref_gene.gtf -o Gb.gtf final.gtf ML.filtered.gtf`...

Multiple samples and single samples produce some transcripts of GTF somewhat differently

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Hi @andrewprzh Thanks in advance. First, suppa2 can get information about alternative splicing events based on GTF files. When I use one sample for Isoquant analysis to get GTF, a...

About RNA methylation difference threshold selection

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@ArtRand When using `modkit dmr` to identify differential m⁶A modifications—similar to differential expression analysis—is it appropriate to use thresholds such as `balanced_effect_size` > 0.2 and `balanced_map_pvalue` < 0.05? Are there...