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Recent Replies
Comment: Troubles launch IGV on Linux(Debian)
by
barslmn
★
1.8k
Great it worked out.
> Any idea why IGV doesn't like it?
No idea but i don't think its on IGV. Wayland is a newer display server for lin…
Comment: How to get ncol = nrow?
by
Devon Ryan
103k
Set the row names to the values of column "X" and then drop column "X". Next time adjust your read.delim or whatever command to automatical…
Comment: Getting the overlap between two GTF files
by
Juke34
8.2k
The script agat_sp_compare_two_annotations.pl or agat_sp_sensitivity_specificity.pl
But if you are interested in the ranges then bedtools…
Answer: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
•
0
@ialbert ,I am deeply immersed in the fog and request the help ,please
Comment: bedtools intersect by position & stand not working even with common regions
by
rfran010
▴
830
are you sure bedtools can handle the non-standard location of strand information?
Answer: Getting the overlap between two GTF files
by
rfran010
▴
830
Maybe somebody knows something I don't, but I feel like bedtools should be able to handle your gtf files directly.
If it's not done alre…
Answer: vcf.gz to vcf
by
Mark
★
1.3k
As the error says, the file is not compressed. In linux the file extension is essentially optional. The file could be named `my.vcf.txt` ye…
Answer: Search RCSB with a list of protein names?
by
Jiyao Wang
▴
340
You can use NCBI esearch to search the protein names against the structure database to get the PDB IDs, then retrieve the structures.
Answer: How to get ncol = nrow?
by
Mark
★
1.3k
Without your actual data, it's hard to assist. I think what you're asking is 'how do I rename the rows of my dataframe(s)'.
Taking the …
Comment: MAKER: WARNING: Could not get initialization lock. Trying Again...
by
GenoMax
134k
What kind of hardware are you running this on? You need to have the right kind of hardware (multiple CPU's not just cores), MPI libraries a…
Answer: Getting the overlap between two GTF files
by
Alex Reynolds
35k
Using `bedops --intersect` and `gtf2bed` will get their common genomic space:
```
bedops --intersect <(gtf2bed < transcripts.gtf) <(gtf2be…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
•
0
```bash
# Obtain the makefile
curl -s http://data.biostarhandbook.com/make/snpcall.mk > Makefile
# Run the makefile
make vcf
```
Error me…
Comment: Encountering Error while Running 'make vcf' in Biostar Handbook
by
Tully
•
0
> System Information: Ubuntu 22.04 (WSL2)
>
> Shell: zsh
>
> Installation Verification: Yes, doctor.py OK
[1]: https://www.biostarhand…
Comment: Retrieve The Reads And Fastq From Bam File
by
Reem
•
0
Did it affect the bamtofastq output file? if so how did you solve the problem?
Thanks
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