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Comment: RNA-seq analysis
by
rfran010
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More info would be useful, such as some example chimeric reads and some numbers to qualify "most" and "very few", but most reads being chim…
Answer: Mageck RRA is listing negative controls as high fold change in the gene summary
by
ltalignani
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OK, thanks a lot, that's the first column.
Comment: Drastic drop in RNA-seq read mapping rate when disabling gaps in Bowtie2
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RSEM does not permit processing alignments with gaps. This is due to the way that the program models read error (using a fixed, position-s…
Comment: Mageck RRA is listing negative controls as high fold change in the gene summary
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jared.andrews07
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The file provided to `--control-sgrna` should contain only the sgRNA IDs in a single column. Currently, you're providing the *gene* IDs. Th…
Comment: The allele with index 2 is not defined in the REF/ALT columns" error after AF fi
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erikatatianacs
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yes, but I think that I need it in this way because the main idea if filter by the population AF, so I dont need the AF of the sample
Comment: Trim CDS to ORF
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Thanks, @lievensterck. I'll look into those to see if they can accommodate the designated offset.
Comment: The allele with index 2 is not defined in the REF/ALT columns" error after AF fi
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by the way, when using bcftools annotate this way, you would overwrite the original AF field with the value of gnomad.
https://samtools.…
Answer: Trim CDS to ORF
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lieven.sterck
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Why not use an ORF finder tool?
eg. getORF , longestORF, transdecoder, FrameD, ... many options. Unless yo have prior knowledge on your t…
Comment: The allele with index 2 is not defined in the REF/ALT columns" error after AF fi
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there was already a problem before bcftools nom . Do you still have two alleles in sample_raw.vcf.gz at the same position ? if true you s…
Answer: Mageck RRA is listing negative controls as high fold change in the gene summary
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ltalignani
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I'm having the same problem: in my `gene_summary.txt`, these negative controls appear.
I used the following script:
#!/bin/bas…
Comment: Obtaining Q30/Q60 Values from Fastq Files
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joe_genome
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thanks that makes sense! thanks for sharing the link!
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Thanks for the troubleshooting !
> Seurat::RunPCA forces the usage of the scale.data layer. And it disables centering (center = NULL)
The…
Comment: RNASeq bulk transcriptomics analysis
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just out of curiosity, and for completeness, can you provide the numbers that you used to get to the 'only 37% mapped' result?
Comment: RNASeq bulk transcriptomics analysis
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lieven.sterck
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Hopefully, because there aren't any other explanations :)
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