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Recent Replies
Comment: Depth in Cram file does not match depth in VCF file
by
Jeremy Leipzig
23k
can you show us that line in the VCF:
`cat PC_1-7.wf_snp_clinvar.vcf | grep 69078931`
Comment: Lacking exons in gtf file of a virus' genome
by
GenoMax
150k
Since the host is always going to be there you can do the mapping to a combined three transcriptome pool, as a test/first-pass. That will g…
Comment: Good QC Package (RSeQC or alternative) for Salmon mapping/quantification results
by
squidqid
•
0
Did you ever get an answer to this question?
Comment: Lacking exons in gtf file of a virus' genome
by
ZuelTech
•
0
I mean, can I map all lists of the libraries ( HAZV-infected, LGTV-infected, uninfected) to the HAZV genome? Can I also map them to the LGT…
Comment: Lacking exons in gtf file of a virus' genome
by
GenoMax
150k
> Then, I want to map the libraries to each of the virus genome. Is this possible?
Possible but will that be logical. If you have all thr…
Comment: Lacking exons in gtf file of a virus' genome
by
ZuelTech
•
0
Thank you! Btw, going back to mapping, I’m working with a vector infected with HAZV and LGTV virus. I have libraries with the host infected…
Comment: Lacking exons in gtf file of a virus' genome
by
Michael
55k
Yes, that you can do as well. Then you don't need to use STAR. But I would add the host transcriptome as a decoy there.
Comment: Lacking exons in gtf file of a virus' genome
by
ZuelTech
•
0
I see, thank you so much! I’ll try this method. Can I also use Salmon in quantification?
Comment: Lacking exons in gtf file of a virus' genome
by
Michael
55k
> Does it mean I don’t need to put a gtf file when I do mapping to HAZV
> genome?
Indeed, unless you want to generate the count file in ST…
Comment: Lacking exons in gtf file of a virus' genome
by
ZuelTech
•
0
Thank you! I’m new to bioinformatics, particularly on working with virus. What can you recommend on what to do with mapping with the reads …
Comment: Lacking exons in gtf file of a virus' genome
by
ZuelTech
•
0
Thank you. But I think the one you provided is from Refseq (as evident from the file name “GCF…”, mine I used the genome from GenBank with …
Answer: Lacking exons in gtf file of a virus' genome
by
Michael
55k
If there are no exons, that means that the annotators didn't consider splicing relevant. This is common for bacteria and viruses. Therefore…
Comment: Lacking exons in gtf file of a virus' genome
by
GenoMax
150k
You can find the GTF file here --> https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/002/831/085/GCF_002831085.1_ASM283108v1/
Be sure to get th…
Comment: Lacking exons in gtf file of a virus' genome
by
ZuelTech
•
0
No transcriptome available. I'm particularly using a virus genome. I need to perform indexing and mapping using STAR. Is there a way to kno…
Comment: Lacking exons in gtf file of a virus' genome
by
ATpoint
87k
If no proper annotations are present in terms of GTF, is there a transciptome fasta available? Then you could quantify with something like …
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