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Hi,
Thank you for the script, I have got it to run and it has all the essential information. Through the IDs the other metadata can anyway be matched.
However, there is one tiny problem: The origin…
arpoe updated
4 years ago
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Hi Ian,
Thanks very much for this program - overall it's done a great job of our plastid genome (and it's so fast!).
I have a feature request, if possible. I noticed that for one of our genes, t…
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**Snakemake version**
7.21.0
**Describe the bug**
Hi,
I have the following rule which contains both Python code and shell commands.
```python
rule run_mags_prodigal:
input:
mag…
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I ran the pipeline on my laptop like this:
``` sh
time sh lincRNA_pipeline.sh -c sample.data/cuffcompare_out_annot_no_annot.combined.gtf -g sample.data/Brapa_sequence_v1.2.fa -r sample.data/Brassica_…
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Hi,
First of all, thanks you for the nice program you design and wrote!
Observation: It seems that transcript features annotated using CPAT and DIAMOND identify ORF and annotate transcripts usi…
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Hey! I do have another question!
After annotating my MAGs, I saw that FeGenie didn't find any transport-related clusters in any of my MAGs, which wouldn't make sense biologically (I have, among o…
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I assume you parse the diamond output to somehow generate the count tables? I am wondering how you do this as I would like to know on what contigs the genes were found so I can generate a pseudo abund…
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### Description
We are using OpenROAD (with ORFS) to tape out on a proprietary PDK. The cell library contains endcap, corner and tbtie cells that contain a metal1 ring (that needs to be connected to …
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Hello,
We are noticing that the ORFs called in 1.5.1 are different than 1.6.1.
Also, we are seeing +, *, and # randomly being put in sequences in 1.6.1.
I assume that the * are stop codons?
W…
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I have ran trinity based fusion transcript denovo assembly, but I am wondering is there a way to identify the fusion break point within this transcript sequence? In another words, if I have a fusion t…