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Comment: How to insert dbSNP in a database?
by
magnolia
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0
Thank you!
1) I need this because I want to connect all the data I need query via SQL.
2) Thanks a lot but this file only has 200 million…
Comment: The best way to get gene lengths for 15K+ genes?
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rpolicastro
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You should first ensure that calculating TPMs like this is valid for your analysis. Proper TPMs generally need to be calculated from transc…
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chronotope
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Hey!
I tried the script, but I am getting this error:
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SLF4J: Defaultin…
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My criteria for whether it makes sense would be comparing MAPQ values for alignments when using reference genome vs expanded genome. If the…
Comment: Warning - longer object length is not a multiple of shorter object length
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JACKY
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Thanks!
Do you also think my genelength calculation method is slumpy?
What do you think about this approach?
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FAQ: https://kb.10xgenomics.com/hc/en-us/articles/360001074271-Does-Cell-Ranger-automatically-exclude-doublets-
Comment: Expanding reference genome with alt loci and decoy sequences
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Yes, technically you can append any sequence to the reference followed by building a new index. If that makes sense or is appropriate is a …
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for example edgeR see https://support.bioconductor.org/p/64585/
Refer to https://www.biostars.org/p/115674/ , https://www.ncbi.nlm.nih.go…
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1) why do you need this ?
2) you can always upload the UCSC dbsnp files. ex.:
http://hgdownload.cse.ucsc.edu/goldenpath/hg19/databas…
Comment: Finding out if a query sequence is present in a read library / bam file (blast a
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thanks! I will try it out today
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Check out [this][1] discussion on gene length in DESeq2.
[1]: https://support.bioconductor.org/p/67131/
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A proven Bioconductor package you mean using a package for normalization?
If so, is there any package you recommend ?
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Did you adjust this setting in the maker_opts.ctl file?
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Hey you can use stlearn package in Python, create an ANN object manually using function
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