ribotricer

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Unannotated ORFs

6

Hi there! I have a question about how RiboTricer handles unannotated sequences. **Purpose**: I am trying to run RiboTricer after generating BAM files using SQUIRE (which does both gene and...

singhbhavya

Prepare ORFs step

1

I had a question regarding preparation of all candidate ORFs from annotated transcript regions. I was wondering why only 3 frame translation is conducted to pull out candidate ORF. If...

bshim181

[BUG] speficying unstranded data ('no') leads to error

3

* ribotricer version: 1.3.3 * Operating System: Linux ### Description Just experimenting with `--stranded` ### What I Did ``` ribotricer detect-orfs \ --bam SRX11780888_chr20.bam \ --ribotricer_index homo_sapiens_chr20_candidate_orfs.tsv \ --stranded no...

pinin4fjords

* ribotricer version: 1.3.3 * Python version: 3.10.12 * Operating System: GNU bash, version 5.0.17(1)-release (x86_64-pc-linux-gnu) ### Description I have two sample to detect orfs. One is done but another...

fork16

Ribotricer Output

4

Hello, I am trying to merge two list of ORFs predicted by the RibORF algorithm and Ribotricer Algorithm. I am aware that RibORF predicts ORFs at the transcript level while...

bshim181

ORF Annotations

1

Hello, I was wondering if there is a way to further break down ORF annotations presented by the ribotricer algorithm. I would like to get a sense for proportion of...

bshim181

p-site offsets and metagene profiles

5

Hi Saket, Thanks for developing this great tool! I am surprised to get these results for the `psite_offsets.txt`output file: ``` relative lag to base: 33 lag of 28: 0 lag...

p-levy

Internal ORFs

2

I was wondering why Ribotricer does not have an ORF category that is called "internal". I was trying to compare results for ribotricer and ribocode and I identify an internal...

annebresciani

Allow input of already p-shifted reads (bigwig)

3

**Is your feature request related to a problem? Please describe.** This tool can not input already shifted data, makes it less useful for the community, since sometimes large bigwig files...

Roleren

the result of the translating ORFs.tsv

1

Hi,When I ran ribotricer and obtained the translating_orfs.tsv results, I noticed that the first row shows a value of 568 in the valid_codons column. This number cannot be divided evenly...

1127yangyuping