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Recent Replies
Answer: ERROR When Using Ensembl Plants Biomart Wget API
by
Ben_Ensembl
★
2.4k
Hi Dora,
For plant species such as *A. thalina*, you should use the http://plants.ensembl.org/biomart service, so the start of your wget…
Answer: Introduce SNPs on FASTA
by
christopher medway
▴
450
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
by
Michael
54k
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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Riccardo
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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!
Comment: unable to get feature count results
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GenoMax
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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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GenoMax
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If you have specific changes you want to make then you can edit the fasta file accordingly.
Answer: Taking the difference of two VCFs (or removing singletons)
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Andres
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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. …
Comment: NGS forensics: how to know if data is fabricated
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i.sudbery
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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…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
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.
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac
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David Langenberger
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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
by
Patadu94
•
0
Oh, then I will check the output file from featureCounts.
Comment: Low mapping rate with Salmon
by
Patadu94
•
0
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…
Answer: Deseq2
by
Jack Tierney
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360
[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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