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## Part 1: Bash Script for Bedtools Commands (2.5 pts)
You did not submit the shell script for creating the feature bed files using `bedtools`. This was required to get full credit for Part 1.
Sco…
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**Is your feature request related to a problem? Please describe.**
A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
**Describe the solution you'd like**…
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Hello,
I'm running some Vitaceae transcriptome data with Arabidopsis as ref, I got warning as below:
Warning: lcl|Query_10114 AT3G08520: Warning: Could not calculate ungapped Karlin-Altschul paramet…
ghost updated
7 years ago
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The position converter for the version 2 of mutalyzer was great at distinguishing between transcripts, but now does not seem to provide that function easily. Is it possible to have the previous featur…
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Hi,
I get an error trying to read gif files using `rtracklayer::import(< gtf file>, format="gtf")`. The same error occurs when I don't specify the format.
```
> library(rtracklayer)
> rtrackla…
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Hello, I want to make pcr primers for a several different genomes to make PCR in one pool. Maybe I am a little bit stupid, but I dont understand, is there a way how to do it with your program? Will NG…
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Hi team
Thanks for the great toolkit. I was wondering if this could be updated to work with later Ensembl vep releases (the latest as of Feb 2023 is 109.3 - https://github.com/Ensembl/ensembl-vep/r…
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Hi,
I keep encountering an error while running JUM step A. I am using JUM 3.0.0.
The error is:
"ERROR: Sort order was unspecified, and file treat1Aligned.out.sorted.bed is not sorted lexicograph…
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## Bug Report
### Affected tool(s) or class(es)
HaplotypeCaller
### Affected [Version 4.1.5.0](https://github.com/broadinstitute/gatk/tree/4.1.5.0)
- [GATK 4.1.5.0 ] public release version
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Hello, professor
I am a graduate student studying cfRNA-seq.
First of all, thank you for posting a good pipeline.
I'm writing like this to ask you if you used ercc.fa, ercc.gtf when making ER…