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Recent Replies
Answer: Introduce SNPs on FASTA
by
christopher medway
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You could take a look at the mutfa command in [seqtk][1]
[1]: https://docs.csc.fi/apps/seqtk/#usage
Answer: Introduce SNPs on FASTA
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If you have a VCF file with all the ALT alleles that you need to insert and a reference genome in FASTA, you can use [bcftools consensus][1…
Comment: Introduce SNPs on FASTA
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Thank you very much. Is there a script or program that does it automatically?
Comment: Post-imputation plot
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kl
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This does not warrant redoing the imputation, though? Do you have any advice of what to take care of, in this circumstance? Thanks!
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Galaxy specific questions are best posted to their support site: https://help.galaxyproject.org/
That said, problems with counting are lik…
Comment: Introduce SNPs on FASTA
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If you have specific changes you want to make then you can edit the fasta file accordingly.
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I know this is an old question but when searching for filtering out singletons(and doubletons too) i found this post in the first results. …
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In which case, I'd definately look at the distribution of read lengths, post trimming, and see if there is a discontinuity in the distribut…
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I would note that even on a good, polyA selected, RNA-seq run, I would only expect 60-75% of mapped reads to map to protein coding exons.
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:: FINAL CALL :: 8th Berlin Summer School in NGS Data Analysis 2024 - Only a few last places available
Comment: Low mapping rate with Salmon
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Oh, then I will check the output file from featureCounts.
Comment: Low mapping rate with Salmon
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How would I check if these reads are aligning to regions where there is no expressed sequence know? Should I follow the suggestion of i.sud…
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[This vignette][1] is a great place to start.
[1]: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.ht…
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Thanks, yes i have tried first here looking for a easier solution (for me), i didnt' know if this format was already available somewhere. t…
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