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Recent Replies
Comment: Good QC Package (RSeQC or alternative) for Salmon mapping/quantification results
by
squidqid
•
0
MultiQC is very helpful. From my understanding, however, MultiQC will not parse the information from useful auxiliary outputs like .../aux_…
Comment: Remove batch effect RnaSeq (RUVg)
by
ATpoint
87k
It is generally expected in communities like this that you read the manual first which covers this https://bioconductor.org/packages/releas…
Comment: Good QC Package (RSeQC or alternative) for Salmon mapping/quantification results
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GenoMax
150k
If you are using single cell data then you really should be using `alevin-fry/simpleaf` packages ([**LINK**][1]) instead of `salmon`. There…
Comment: Depth in Cram file does not match depth in VCF file
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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
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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
•
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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
•
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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 …
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