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Recent Replies
Comment: ChatGPT optimized for bioinformatics questions
by
Dr William Klubinski
▴
100
Great initiative :D
Answer: Extract variants/SNPs with T>G substitution from a VCF file
by
4galaxy77
2.7k
Use ```bcftools view``` with the `-i` flag for including variants.
```
bcftools view -i'REF=="T" & AlT == "G"'
```
Comment: A question about the raw RNA-seq processing workflow
by
Dr William Klubinski
▴
100
Hi there, the `Segmentation fault (core dumped)` seems to be related to memory issues. I would check the `core dump` that has been created …
Comment: Ensembl vep singularity
by
Ben_Ensembl
★
2.2k
Hi Kiran - there is a description of downloading and running VEP with Singularity 3.5+ in the following blog post:
https://www.ensembl.inf…
Comment: conda: command not found: gatk.
by
bestone
▴
20
oops I didn't know I was going to evaluate them there, thanks for the warning, now I will evaluate them all. pls, could you pls with this i…
Comment: conda: command not found: gatk.
by
Pierre Lindenbaum
155k
> how about all your previous questions ? take a time to validate the good answers
Comment: conda: command not found: gatk.
by
bestone
▴
20
I was using gatk before, but conda env create -n gatk -f gatkcondaenv.yml didn't run this command, so I wanted to delete gatk and install t…
Comment: conda: command not found: gatk.
by
Pierre Lindenbaum
155k
how about all your previous questions ? take a time to validate the good answers (green mark on the left).
https://www.biostars.org/p/9565…
Answer: No @hd header returned in sam file when running bwa mem
by
Pierre Lindenbaum
155k
the HD header is not generated by bwa, but you can add it using awk:
bwa (...) | awk '(NR==1) {printf("@HD\tVN:1.6\tSO:unknown\n");}{…
Comment: Ensembl vep singularity
by
Kiran
▴
80
Hi I also pulled SIF image from docker,, Now how do i execute the VEP from singularity ?
Answer: No @hd header returned in sam file when running bwa mem
by
GokalpC
▴
80
Your sam file is not coordinate sorted or converted to a bam. @HD tags come after a secondary tool such as samtools view or sort.
ANGSD…
Comment: Mapping a predicted sequence to a genome
by
Mensur Dlakic
★
23k
It may or may not, depending on the exact organism. For example, baker's yeast has introns but not many, and most genes in its genome don't…
Comment: Mapping a predicted sequence to a genome
by
Andy
•
0
Thank you for your answer! If the organism I am studying has introns, will blastn still be sufficient?
Answer: Mapping a predicted sequence to a genome
by
Mensur Dlakic
★
23k
If we are talking about organisms without introns, it is very simple. A tool to use is `tblastn` which can be accessed from the [**main BLA…
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