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The definition states, at the end, that an isoform may differ from other variants owing to post-translational modification. Is this intended to mean exclusively proteolytic cleavages, or does it inclu…
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imagine it is received a string with column names
we need the code to retrieve only those columns from our tables
eg, from the following text line:
`columns = 'reverse,chromosome,start_gene_coord…
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Labelling a mutation as a Missense Mutation suggests that it is expressed as a protein, so would need to be detectable at the RNA level as a pre-requisite. Could the software allow the user to input a…
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Since gff files have specific parent/child structure, they are a natural fit for representing splicing events as isoforms. Additionally, the gff files created by outrigger can be combined with the ori…
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Sorry to bother you.
I followed your workflow use STAR arguments `--quantMode TranscriptomeSAM` and `--outFilterMultimapNmax 1`,this is the command looks like
```
STAR --outFilterType BySJout --run…
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Based on the [MAESTRO paper](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02116-x#Sec12), my understanding is that a peak that is in the exons or promoter region of more than on…
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I am wanting to visualise reads that map to each isoform by using the --generate_map option from collapse. The reads the supposedly support this novel isoform (225532d7-ec74-4839-9708-8c26168366cb_ENS…
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Hi team,
I found your isonform output fasta file is not a standard format with `>` line as header. And there are lots of empty files in the isonform fodler such as
```
(base) [yan.a@vc7-shared i…
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Hi everyone,
I tried to run TOGA using my data and the following command (./toga.py human_mesbid/human.mesbid.final.chain human_mesbid/hg38.wgEncodeGencodeCompV34.bed human_mesbid/hg38.2bit human_m…
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Hi,
Thank you so much for creating DIA-NN. I am new to this tool. I was trying to generate a predicted spectral library from a FASTA file. To access the library properties I loaded it in DIA-NN r…