dudududu12138
dudududu12138
Hello, I use Augustus to predict alternative transcripts. The result is in gff format. But I don't understand the 6th column. It looks like probabilities. But I noticed that the...
Hi, If I have a series of interchromosomal translocation events stored in .vcf file, can I construct a graph that represent this kind of variants using vg ? If vg...
Hello, now I have a Nanopore cDNA sequencing data. And I detected the strands of every reads from the raw data. Then I mapped the reads to hg38 with `minimap2...
Hello, I saw the built-in annotation file ([https://github.com/Illumina/SpliceAI/blob/master/spliceai/annotations/grch38.txt](url)). But I want to make a custom annotation set. And I want to know how did you define exons? I mean, there...
Hi, I want to use bambu(v3.5.1) on single sample while it seems that the parameter `ncore` is applied to improve the efficiency of multisamples. So I tested different combinations of...
Hi, I used bambu on one sample. The alignment result(.bam) of this sample is about 34G. And I run bambu on HPC cluster. I set the cpu number to 20....
Hi, I ran talon with your example data and followed the wiki code(https://github.com/mortazavilab/TALON/tree/master/example). But I compare the transcripts bewteen `example_raw_talon.gtf` and `example_talon_abundance.tsv`. There are 2 more transcripts in `example_raw_talon.gtf` while...
Hi, I recently ran stringtie2 to assemble transcript from long RNA-seq data. My data is a HIFI cDNA data. And I map raw data to GRCh38 with minimap2. Then I...
Hi, I used gffcompare to merge multiple assemble results from different samples. The code is listed below: ``` gffcompare -T -S $gffcompare_inputs -o $output ``` I didn't offer a reference...
Hi, I have a graph that constructed directly from aligned de novo assemblies. I used it as a reference and aligned short reads to this graph with `vg giraffe`. Then...